• Marine-derived nutrients in riverine ecosystems: developing tools for tracking movement and assessing effects in food webs on the Kenai Peninsula, Alaska

      Rinella, Daniel J. (2010-05)
      Marine-derived nutrients (MDN) delivered by spawning Pacific salmon (Oncorhynchus spp.) contribute to the productivity of riverine ecosystems. Optimizing methods for measuring MDN assimilation in food webs will foster the development of ecologically based resource management approaches. This dissertation aims to better understand relationships among spawning salmon abundance, biochemical measures of MDN assimilation, and the fitness of stream-dwelling fishes. The goals of my first research chapter were (1) to understand the factors that influence stable isotope ([delta]¹³C, [delta]¹⁵N, and [delta]³⁴S) and fatty acid measures of MDN assimilation in stream and riparian biota, and (2) to examine the ability of these measures to differentiate among sites that vary in spawning salmon biomass. For all biota studied, stable isotopes and fatty acids indicated that MDN assimilation increased with spawner abundance. Among Dolly Varden (Salvelinus malma), larger individuals assimilated proportionately more MDN. Seasonal effects were detected for aquatic macroinvertebrates and riparian horsetail (Equisetum fluviatile), but not for Dolly Varden. Of all dependent variables, Dolly Varden [delta]¹⁵N had the clearest relationship with spawner abundance, making this a good measure for monitoring MDN assimilation. Expanding on these results, two chapters examined potential fisheries management applications. The first sought to identify spawner levels above which stream-dwelling Dolly Varden and coho salmon (O. kisutch) parr cease to gain physiological benefits associated with MDN. RNA-DNA ratios (an index of recent growth rate) and energy density indicated saturation responses where values increased rapidly with spawner abundance up to approximately 1 kg/m² and then leveled off. In coho salmon parr, energy density and RNA-DNA ratios correlated significantly with [delta]¹⁵N. These results show strong linkages between MDN and fish fitness responses, while the saturation points may indicate spawner densities that balance salmon harvest with the ecological benefits of MDN. The second application tested a quick and inexpensive method for estimating, spawning salmon abundance based on [delta]¹⁵N in stream-dwelling fishes. Estimates made with coho salmon pair were unbiased, tightly correlated with observed values, and had a mean absolute deviation of 1.4 MT spawner biomass/km. Application of this method would allow estimates of annual escapement to be made on a potentially large number of streams.
    • Mechanism of impact and potential recovery of pigeon guillemots (Cepphus columba) after the Exxon Valdez oil spill

      Seiser, Pamela (2000-05)
      The abundance of pigeon guillemots in oiled areas of Prince William Sound, Alaska, failed to increase after the 1989 Exxon Valdez oil spill. Population growth may be constrained by the physiological effects of oil exposure, food availability, and nest predation." The author "conducted a comparative study among unoiled, oiled, and pre-spill data sets, to provide insight on factors limiting population recovery in oiled areas. Blood samples from chicks in oiled and unoiled areas provided little evidence of physiological effects of exposure to oil. Pigeon guillemot diet, productivity, growth rates, and fledging weights in unoiled areas of southwestern Prince William Sound from 1994 to 1998 indicate oiled areas had a lower proportion of high-lipid fish in the chick diet and lower fledging weights, compared to unoiled and pre-spill studies. These results suggest that the lack of recovery in oiled areas is associated with a prey base that results in lower fledging weights, which may reduce juvenile survival.
    • The migration and spawning distribution of sockeye salmon within Lake Clark, Alaska

      Young, Daniel B. (2004-08)
      Recent declines in the number of sockeye salmon Onchorynchus nerka returning to Lake Clark, Alaska have caused economic hardship in the region and raised resource concerns among local subsistence users and Federal managers. A lack of information regarding the distribution of spawning habitats in the glacially turbid Lake Clark watershed instigated this research. Radio telemetry was used to 1) determine the in-lake movement patterns of adult sockeye salmon and 2) identify sockeye salmon spawning locations. Sockeye salmon were radio tagged at they entered Lake Clark and tracked to spawning locations. After entering Lake Clark, sockeye salmon usually migrated to a region of the lake that was within 15 km of their spawning location. Tagged fish migrated faster and more directly to spawning locations in tributary rivers and lakes than to Lake Clark beaches. Thirty three spawning locations were identified in the Lake Clark watershed including 18 new spawning locations compared to previous scientific research and ten compared to traditional local knowledge. Most radio tagged sockeye salmon (65%) returned to spawning locations in glacially turbid waters and most spawning locations (75%) were adjacent to privately owned lands. Proactive measures should be taken to conserve both migration corridors and spawning habitats.
    • Migration ecology and distribution of king eiders

      Phillips, Laura Marie (2005-08)
      Alaskan-breeding king eiders (Somateria spectabilis) disperse from nesting areas on the Arctic Coastal Plain and move through the Beaufort Sea to wing molt and winter locations in remote areas of the Bering Sea. Knowledge of king eider distribution outside the breeding period is critical to provide regulatory agencies with opportunities to minimize potential negative impacts of resource development. To characterize the nonbreeding distribution of king eiders, we collected location data of 60 individuals over two years from satellite telemetry. During post-breeding migration, male king eiders had much broader use areas in the Alaskan Beaufort Sea than female eiders. Chronology of wing molt was earlier for males than females in all years. Throughout wing molt and winter, eider locations were closer to shore, in shallower water with lower salinity than randomly selected locations. Short residence time of king eiders in deep water areas suggests the Alaskan Beaufort Sea may not be as critical a staging area for eiders during spring as it is during post-breeding. This study provides some of the first large-scale descriptions of king eider migration, distribution, and habitat outside the breeding season.
    • Migratory patterns of Yukon River inconnu as determined with otolith microchemistry and radio telemetry

      Brown, Randy J. (2000-05)
      Migratory patterns of Yukon River inconnu Stenodus leucichthys were evaluated using otolith aging and microchemical techniques and radio telemetry. Research was conducted each fall between 1997 and 1999, on inconnu captured at a study site 1,200 river km from the Bering Sea. Biological data were collected to establish maturity and spawning condition. Sagital otoliths were analyzed optically to determine age distribution, and microchemically to determine amphidromy. Inconnu were tagged with radio transmitters and located in upstream spawning destinations. Inconnu captured at the study site were uniformly large, mature fish preparing to spawn. Age estimates ranged from 7 to 28 years. Microchemical analyses suggested that the population was amphidromous rather than freshwater only. Preliminary testing of radio transmitter attachment methods showed that the internal method (pushed through the esophagus into the stomach) was superior to the external method (attached behind the dorsal fin) for use with migrating inconnu. Most radio-tagged inconnu were located during their spawning time in a common region of the Yukon River. Inconnu captured at the study site each fall were mature fish engaged in a spawning migration that originated in the lower Yukon River or associated estuary regions, and continued towards a common spawning destination in the Yukon River, approximately 1,700 river km from the sea.
    • Modeling stand-level canopy maintenance respiration of black spruce ecosystems in Alaska: implications for spatial and temporal scaling

      Zhang, Xinxian (2001-05)
      Canopy respiration represents an important part of the carbon budget of black spruce forests. In this study I scaled hourly models of foliar maintenance respiration (Rm) to estimate canopy Rm for individual stands, and investigated issues in scaling the models to estimate canopy Rm using mean monthly temperature data. I used data from several stands to develop hourly stand-specific and stand-independent models of canopy Rm. Analysis of stimulated canopy Rm indicated that stand-level controls over foliar N concentration should be considered in models that estimate canopy Rm of black spruce stands across the landscape. Uncertainty analyses indicated that the parameter that describes maintenance respiration rate at 0C̊ per g N has the greatest influence on annual estimates of canopy maintenance respiration. Finally, comparisons of monthly Rm between the hourly and monthly versions of the models indicated that mean monthly temperature can be used to drive models of canopy Rm with little loss of precision.
    • Modeling The Influences Of Climate Change, Permafrost Dynamics, And Fire Disturbance On Carbon Dynamics Of High -Latitude Ecosystems

      Zhuang, Qianlai; McGuire, A. David (2001)
      A Soil Thermal Model (STM) with the capability to operate with a 0.5-day internal time step and to be driven with monthly input data was developed for applications with large-scale ecosystem models. The use of monthly climate inputs to drive the STM resulted in an error of less than 1�C in the upper organic soil layer and in an accurate simulation of seasonal active layer dynamics. Uncertainty analyses identified that soil temperature estimates of the upper organic layer were most sensitive to variability in parameters that described snow thermal conductivity, moss thickness, and moss thermal conductivity. The STM was coupled to the Terrestrial Ecosystem Model (TEM), and the performance of the STM-TEM was verified for the simulation of soil temperatures in applications to black spruce, white spruce, aspen, and tundra sites. A 1�C error in the temperature of the upper organic soil layer had little influence on the carbon dynamics simulated for a black spruce site. Application of the model across the range of black spruce ecosystems in North America demonstrated that the STM-TEM has the capability to operate over temporal and spatial domains that consider substantial variations in surface climate. To consider how fire disturbance interacts with climate change and permafrost dynamics, the STM was updated to more fully evaluate how these factors influence ecosystem dynamics during stand development. The ability of the model to simulate seasonal patterns of soil temperature, gross primary production, and ecosystem respiration, and the age-dependent pattern of above-ground vegetation carbon storage was verified. The model was applied to a post-fire chronosequence in interior Alaska and was validated with estimates of soil temperature, soil respiration, and soil carbon storage that were based on measurements of these variables in 1997. Sensitivity analyses indicate that the growth of moss, changes in the depth of the organic layer, and nitrogen fixation should be represented in models that simulate the effects of fire disturbance in boreal forests. Furthermore, the sensitivity analyses revealed that soil drainage and fire severity should be considered in spatial application of these models to simulate carbon dynamics at landscape to regional scales.
    • Molecular and morphological perspectives on post-glacial colonization of Clethrionomys rutilus and Clethrionomys gapperi in Southeast Alaska

      Runck, Amy Marie (2001-05)
      Pleistocene events had a significant impact on the geographic distributions of high latitude organisms. Recently deglaciated, Southeast Alaska has been colonized by two species of red-backed voles, clethrionomys rutilus and C. gapperi. With distinct biogeographic histories, post-glacial colonization of C. rutilus and C. gapperi into this region would have occurred by different routes. Variation in the mitochondrial cytochrome b gene, the MYH2 nuclear intron, and the post palatal bridge were assessed to examine phylogeographic patterns of these two species, and a proposed contact zone in southeast Alaska. Low, but consistent, levels of sequence divergence of the cytochrome b gene were found among four endemic populations, which corresponded with the complex topography of southeast Alaska. Asymmetrical introgression of the mitochondrial genome diagnostic of C. rutilus was observed in C. gapperi. Post glacial contact resulting from the retreat of the Cordilleran and Laurentide ice sheets has apparently led to the formation of this hybrid zone.
    • Molecular evolution of martens (genus Martes)

      Stone, Karen Denise (2000-08)
      Molecular studies provide the opportunity to re-evaluate and further investigate hypotheses such as those related to phylogenetic relationships, inter- and intra-continental colonizations, population differentiation, and the dynamics of hybrid zones. Three sets of molecular markers, nuclear and mitochondrial, were used to examine phylogenetic relationships among species within a holarctically distributed genus (Martes), and intraspecific diversification and population differentiation within American marten (Martes americana). In American marten, two morphological groups ('americana' and 'caurina') have been recognized, though the level of distinctiveness between them has been debated. My data supported the fossil record's indication that early radiations gave rise to two subgenera of the genus Martes (Pekania and Charronia) and that a more recent, possibly rapid, radiation gave rise to species of the third subgenus (Martes). Two colonizations of North America are evident, one by members of the subgenus Pekania, and another by the subgenus Martes. However, contrary to hypotheses based on morphological evidence, the 'americana' and 'caurina' subspecies groups of Martes americana represent only one colonization. Cytochrome b data were consistent with the recognition of these as monophyletic clades; however, aldolase C sequences and microsatellite data indicated that these generaly parapatric groups interbreed in at least one region of limited geographic overlap. These clades probably were isolated during the late Pleistocene in eastern and western refugia, but geographic separation apparently has not led to reproductive isolation. My data also indicated two colonization events for the Pacific Northwest by American martens (one by each clade). Due to patterns of genetic variation, I hypothesize that the 'caurina' clade spread along the North Pacific Coast, including southeastern Alaska, earlier than the 'americana' clade, and that these clades have now formed a zone of secondary contact on Kuiu Island in southeastern Alaska. Microsatellite data revealed population differentiation among many island populations in the Pacific Northwest, but possible gene flow among several near-shore island and mainland populations was suggested. Analyses of genetic and geographic distances suggested that colonization history had a strong effect on present day population structure and that oceanic straits and possibly other physiographic features posed significant barriers to gene flow.
    • Molecular phylogenetics of arvicoline rodents

      Conroy, Christopher John; Cook, Joseph A. (1998)
      The impetus for this dissertation was an interest in geographic variation in Microtus longicaudus with a particular focus on populations in the Alexander Archipelago of southeastern Alaska. To establish a framework for interpreting intraspecific variation in M. longicaudus, I examined the phylogenetics of 28 species of the genus Microtus, including all North American species (Chapters 2 and 4). That study, which corroborates a rapid pulse of diversification noted in the fossil record, necessitated a deeper phylogenetic perspective. Thus, a third objective of the dissertation was to investigate relationships among genera of arvicolines within the framework of other murid rodents. I examined variation in the mitochondrial cytochrome b and ND4 genes using maximum parsimony, distance, and maximum likelihood phylogenetic analyses. Relationships at several taxonomic levels appear intractable due to rapid accumulation and survival of genetic lineages. These rapid radiations were found among species, genera, and possibly subfamilies; however, strong support at these levels for other taxa (e.g., the monophyly of Microtus) suggests these genes have strong phylogenetic signal. Many of the well-supported sister species pairs within Microtus (Chapters 2 and 4) had been previously identified based on morphologic or allozyme work (e.g., M. pennsylvanicus and M. montanus, M. pinetorum and M. quasiater). The sequence data supported a clade of taiga dwelling species in North America and a clade of eastern and central Asian species. The southernmost arvicoline species of Mexico and Guatemala, though previously suggested to be derived from a single ancient invasion, did not appear to be either ancient or monophyletic. Within M. longicaudus, a large east-west phylogeographic break was detected that is equivalent in genetic distance to other sister species pairs in the genus. This break may indicate mid to late-Pleistocene differentiation (Chapter 3) within the genus. At higher latitudes, populations of M. longicaudus exhibited evidence of recent range expansion including absence of correlation between geographic and genetic structure; and pairwise mismatches among DNA sequences with a single peak and few differences.
    • Molecular systematics and biogeography of long-tailed shrews (Insectivora: Sorex) and northern flying squirrels (Rodentia: Glaucomys)

      Demboski, John Richard; Cook, Joseph A. (1999)
      Insight into phylogenetic and biogeographic relationships among several mammalian taxa in western North America was provided with DNA sequences of two mitochondrial genes (cytochrome b and ND4). Members of two species complexes of long-tailed shrews (genus Sorex ) and northern flying squirrels (genus Glaucomys) were examined, and a common theme of responses to past climate change and glacial cycles was evident. Diversification events indicated by the DNA sequences provide new perspectives regarding the deep and shallow history of these taxa. Analysis of seven species of the Sorex cinereus complex (and related species) revealed two major clades within the complex, Northern and Southern. These generally corroborate proposed morphological relationships and correspond to broadly defined habitat affiliations (xeric and mesic), respectively. Within the Northern clade, amphiberingian species represented a monophyletic group suggesting Beringia was a center of endemism. Next, five species of the S. vagrans complex and related species were assessed. Significant molecular variation was revealed that does not correspond to morphological differences within the complex. Two major clades within S. monticolus were observed, a widespread Continental clade (Arizona to Alaska, including S. neomexicanus) and a restricted Coastal clade (Oregon to southeast Alaska, including S. bairdi and S. pacificus). A regional examination of genetic variation in the northern flying squirrel in southeast Alaska was also performed. Results suggested that southern islands in the Alexander Archipelago were the result of recent colonization (founder event). Finally, a comparative phylogeographic analysis of a reduced data set (S. monticolus), a molecular data set for the American Pine Marten, Martes americana, and other published molecular studies were used to reexamine the role of glacial refugia in the biogeography of the north Pacific coast. Previous ideas regarding purported refugia may be overstated and may be the result of limited geographic sampling. This thesis provides new perspectives on processes (e.g., post-glacial colonization) driving mammalian phylogenetic and biogeographic structuring in western North America.
    • Monitoring energy and nitrogen availability for Arctic caribou (Rangifer tarandus)

      VanSomeren, Lindsay L.; Barboza, Perry S.; Bret-Harte, M. Sydonia; Gustine, David D. (2014-12)
      Arctic caribou and reindeer (Rangifer tarandus) are an economically and ecologically important species. Rangifer populations are often affected by nutritional factors. Our ability to monitor nutrient supply to arctic ungulates is presently limited by a lack of techniques to consistently and easily measure availability of specific nutrients and which may disproportionately affect different segments of Rangifer populations. I refined and validated a method to measure availability of specific nutrients including nitrogen (N) and energy to caribou using purified fibrolytic enzymes and acid/pepsin to simulate digestion. I then used this method to measure how availability of nitrogen and energy was altered by anti-nutrients such as indigestible fiber and toxins. Digestible N contents in forages declined to almost zero by the end of the growing season, whereas digestible energy concentrations were still sufficient to meet basic maintenance requirements for caribou by the end of the growing season in shrub and forb forages. Shrubs contained the highest amounts of total N and energy, however this was reduced by fiber and toxins so that shrubs contained the lowest digestible N contents, especially for Betula nana. Graminoids were extremely low in digestible energy content, which may necessitate a high degree of selection among plant parts by herbivores. Dietary choice over long- and short-term periods may be assessed using non-invasive stable isotope techniques, nevertheless, the understanding of how isotopic signatures vary over spatial, temporal, and species-specific scales and how isotopic signatures are changed by digestive processes is limited. Monocot (graminoid) and dicot (browse and forb) forages both differed in values of 13C and 15N, however regional and seasonal shifts in 13C were larger than the differences among forage groups themselves. Forage isotopic signatures also changed after simulated digestive processes, yet this was only significant for species with very low (< 52.6 % N) or very high (> 36.6 % C) digestibilities. These studies suggest that nitrogen may be a limiting nutrient for caribou populations. Persistence of arctic caribou populations in a changing climate may depend, in part, upon continued access to calving grounds, the change in abundance of individual shrub species, and/or the ability of caribou to behaviorally and physiologically cope with increasing amounts of toxins in shrubs.
    • Moose (Alces alces) browse availability and use in response to post-fire succession on Kanuti National Wildlife Refuge, Alaska

      Julianus, Erin L.; McGuire, A. David; Nettleton Hollingsworth, Teresa; Kielland, Knut (2016-08)
      I examined post-fire moose habitat dynamics on Kanuti National Wildlife Refuge in interior Alaska with the objective of increasing understanding of local moose habitat characteristics. I estimated browse density, biomass, and summer browse use in a 2005 burn, 1990 burn, 1972 burn, and an unburned area. I revisited each site the following spring to estimate browse availability and removal during winter. In addition to evaluating browse production and use, I estimated proportional habitat use of varying-aged burns by 51 VHF-collared moose. I found that summer browse production and winter browse availability were highest in the 1990 and 2005 burns. I found that summer and winter browse use was highest in the 1990 burn. Collared moose generally avoided recently burned stands and demonstrated preference for >30 year old stands in both summer and winter. Moose demonstrated preference for unburned stands during calving. Although biomass production and availability were highest in 11 – 30 year old stands, disproportionate use of food resources in burns was evident. This disproportionate use of burns and food resources could be due to a variety of reasons including resource type, historic moose distribution patterns, and predation avoidance strategies.
    • Nesting ecology of migratory golden eagles (Aquila chrysaetos) in Denali National Park, Alaska

      McIntyre, Carol L. (1995-12)
      Between 1988 and 1993 I measured occupancy of nesting territories and reproduction of golden eagles (Aquila chrysaetos) in Denali National Park, Alaska. I collected data occupancy of nesting territories and three reproductive variables (pairs nesting, pairs producing fledglings, and fledgling production) at 74 nesting territories using three aerial surveys each year. During my study, annual fledgling production varied nearly threefold, from 20 fledglings in 1992 to 58 fledglings in 1989. Although rates of nesting territory occupancy did not vary significantly among years (yj = 8.21, d.f. = 5, P = 0.114), I noted significant variation in the proportion of pairs laying eggs (X2 = 33.12, d.f. = 5, P < 0.001) and the proportion of pairs fledging young (X2 = 16.03, d.f. = 5, P = 0.007) among years. Decreases in pairs laying eggs were correlated with decreases in average daily numbers of snowshoe hare (Lepus americanus) and willow ptarmigan (Lagopus lagopus) observed in the study area (rs = 0.83, P = 0.04).
    • New 3-d video methods reveal novel territorial drift-feeding behaviors that help explain environmental correlates of Chena River chinook salmon productivity

      Neuswanger, Jason; Rosenberger, Amanda E.; Evenson, Matthew J.; Adkinson, Milo D.; Bradford, Michael J. (2014-08)
      Chinook salmon (Oncorhynchus tshawytscha) are critical to subsistence and commerce in the Yukon River basin, but several recent years of low abundance have forced devastating fishery closures and raised urgent questions about causes of the decline. The Chena River subpopulation in interior Alaska has experienced a decline similar to that of the broader population. To evaluate possible factors affecting Chena River Chinook salmon productivity, I analyzed both population data and the behavior of individual fish during the summer they spend as fry drift feeding in the river. Using a stereo pair of high definition video cameras, I recorded the fine-scale behavior of schools of juvenile Chinook salmon associated with woody debris along the margins of the Chena River. I developed a software program called VidSync that recorded 3-D measurements with sub-millimeter accuracy and provided a streamlined workflow for the measurement of several thousand 3-D points of behavioral data (Chapter 1). Juvenile Chinook salmon spent 91% of their foraging attempts investigating and rejecting debris rather than capturing prey, which affects their energy intake rate and makes foraging attempt rate an unreliable indicator of foraging success (Chapter 2). Even though Chinook salmon were schooling, some were highly territorial within their 3-D school configurations, and many others maintained exclusive space-use behaviors consistent with the population regulatory effects of territoriality observed in other salmonids (Chapter 3). Finally, a twenty-year population time series from the Chena River and neighboring Salcha River contained evidence for negative density dependence and a strong negative effect of sustained high summer stream discharge on productivity (Chapter 4). The observed territoriality may explain the population's density dependence, and the effect of debris on foraging efficiency represents one of many potential mechanisms behind the negative effect of high stream discharge. In combination, these findings contribute to a statistically and mechanistically plausible explanation for the recent decline in Chena River Chinook salmon. If they are, in fact, major causes of the decline (other causes cannot be ruled out), then we can be tentatively hopeful that the population may be experiencing a natural lull in abundance from which a recovery is possible.