• 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.
    • Habitat use of Pacific herring (Clupea pallasii) in Prince William Sound, Alaska

      Kelly, Seanbob R. (2007-12)
      To determine the spawning area contributions of Pacific herring (Clupea pallashii) larvae to nursery bays, otolith chemical analysis was conducted on juvenile fish collected from 1995 to 1997 in Prince William Sound, Alaska. The otolith edge, representing the chemical signature of the known capture location, and the otolith core, representing the unknown spawning ground chemistry, were compared with discriminant function analysis to infer spawning area origin. Chemical signatures of ⁸⁷Sr/⁸⁶Sr, ⁸⁸Sr/⁴⁸Ca, ²⁴Mg/⁴⁸Ca, and ¹³⁸Ba/⁴⁸Ca were used to identify broad spawning regions from inner and outer PWS that persisted for the three years sampling period despite significant interannual variability in otolith edge chemistry within nursery bays. Age of juvenile Pacific herring, age-0, 1, 2, did not significantly affect the otolith edge signatures; thus, this study is able to conclude from the otolith core chemistry that spawning areas do not contribute equally to nursery bays. This is the first demonstration that otolith chemical signatures can be used to identify the important spawning areas of this commercially important species in the Gulf of Alaska coastal areas.
    • Harmothoe imbricata: species complex or complex species?

      Gastaldi, Angela; Lopez, J. Andres; Hardy, Sarah; Kelley, Amanda; Sikes, Derek (2019-05)
      Accurate estimates of species diversity are constrained by cryptic species complexes, in which multiple closely related species are grouped under a single species name due to the absence of clear morphological differences. Cryptic diversity is known to be prevalent in polychaete worms, a mostly marine group commonly known as bristle worms. A recent survey of polychaete diversity discovered that the widespread scale-worm Harmothoe imbricata comprises multiple distinct mitochondrial lineages based on analysis of the Cytochrome c oxidase I (COI) gene, which is often referred to as the 'barcoding' gene. Analyses based solely on DNA sequences from COI may overestimate the number of lineages comprising a cryptic species complex, so it has been recommended that cryptic species investigations incorporate nuclear gene sequences. The goal of this study was to determine whether the incorporation of DNA sequences from the nuclear genome corroborates the designation of H. imbricata as a cryptic species complex. I sequenced segments of COI and five nuclear genes: ITS1, ITS2, H3, and portions of the 18S and 28S genes of H. imbricata and analyzed them using distance measures, maximum likelihood, and Bayesian inference. I compared phylogenetic trees produced from mitochondrial and nuclear DNA sequences, as well as from a combined mitochondrial/nuclear dataset. Harmothoe imbricata was found to include five mitochondrial lineages, whereas the nuclear sequences only supported four well-defined lineages. These results corroborate previous reports showing COIbased cryptic species investigations find more lineages than nuclear DNA based investigations. These results provide additional lines of evidence that H. imbricata is a cryptic species complex. These divergent lineages likely arose after being separated during the last glacial maximum but they are now found in sympatry. A thorough morphological study of H. imbricata populations may reveal phenotypic differences correlated with the genetic lineages identified here.
    • Health and condition of juvenile chinook and chum salmon near the Chena River Dam, Alaska

      Daigneault, Michael Joseph (1997-05)
      During May-June, 1995 and 1996, outmigrating chum salmon, Oncorhynchus keta, and chinook salmon, O. tschawytscha, were captured in the Chena River near the Chena River Lakes Flood Control Project. Fish condition was determined through the investigation of physical injury and scale loss. Except for one sample, the proportion of injured fish was never greater than 7% for chum or chinook salmon. Few injuries were severe. The proportion of chinook salmon with scale loss ranged from 1-33%, most of which were only partially descaled. When significant length differences existed, injured, descaled, and partially descaled fish were always larger than non-injured and non-descaled fish. Arctic grayling (Thymallus arcticus) diet by weight consisted of chum salmon (2%), invertebrates (89%), other fish (3%), and miscellaneous material (6%). Plasma cortisol levels were used as an indicator of the primary stress response of chinook salmon and did not indicate any unusual physiological stress level.
    • Heat And Freshwater Controlling Processes On The Northern Gulf Of Alaska Shelf

      Janout, Markus A.; Weingartner, Thomas; Coyle, Kenneth; Hedstroem, Ketherine; Johnson, Mark; Okkonen, Stephen (2009)
      We examined conditions and processes that control the distribution of heat and freshwater on the northern Gulf of Alaska (GOA) shelf. Cross-shelf heat gradients are weak throughout the year, while salinity gradients are substantial due to the impact of coastal freshwater runoff. Outer shelf water properties are influenced by large anticyclonic eddies, while the inner and middle shelves may be regulated by wind and freshwater runoff dynamics around the Alaska Coastal Current (ACC). On the outer shelf, anticyclonic eddies propagate from the eastern GOA southwestward along the continental slope, where they favor on-shelf (off-shelf) transport of saline and nutrient-rich (fresh and iron-rich) waters Certain along-shelf locations are identified where low-salinity coastal waters are found near the shelfbreak within reach of eddies and may be regions of enhanced cross-shelf freshwater transport. The eddies have lifetimes of ~5 years and increase in size and sea level anomaly west of the Seward Line, which implies more vigorous eddy cross-shelf exchange in the northwestern GOA. By comparison, on the inner shelf the heat and freshwater distribution is dominated by large coastal river runoff, which forces the ACC and controls the vertical distribution of temperatures through stratification. In May 2007, the coastal GOA revealed some of the lowest ocean temperatures since the early 1970s, initiated by strong atmospheric cooling and reduced coastal runoff in November 2006. Stepwise regression shows that 81% of the variability of deep temperatures is explained by salinity stratification and air-sea heat fluxes. Weak baroclinic flow in May 2007 likely aided the cooling through reduced along-shore heat transport. A more detailed examination of heat transport indicated that along-shore heat flux convergence in the ACC may re-supply 10-35% of the heat removed by air-sea fluxes throughout the coastal GOA cooling season, while the annual mean cross-shore heat flux convergence is insignificant. Spatial gradients show increasing heat fluxes from off- to on-shore and from east to west. The cross-shore gradients result from wind speed gradients due to ageostrophic near-shore wind jets near coastal mountains, while the along-shore gradients result from larger-scale pressure systems. While the ACC advects coastal freshwater around the GOA shelf its waters are subjected to disproportional heat loss west of the Seward Line.
    • Heavy metals in the sediments of an arctic lagoon, northern Alaska

      Sweeney, Michael Devlin (1984-12)
      The total abundances of V, Cr, Mn, Fe, Co, Ni, Cu, and Zn in oxic, nearshore sediments of north arctic Alaska, are similar to those of corresponding pristine or pre-industrial-age sediments of many tropical-temperate regions, and thus do not reflect the unique weathering and depositional processes of the Arctic. Laboratory experiments on metal partitioning suggest that about 50% of the metal contents (<20% for V, Cr), which are bound predominantly in Fe oxides, may be mobilized into solution following the onset of reducing conditions at the sediment surface. A three-part extraction design would be effective in discriminating the three major associations of heavy metals in the sediments: easily leachable, Fe hydroxides, and refractory particles, and is recommended for use in monitoring the nearshore Beaufort Sea for future contamination by heavy metals.
    • Hemocyte and tissue changes by crude oil in the blue mussel Mytilus edulis

      McCormick-Ray, M. Geraldine (1983)
      This study examines the effects of Prudhoe Bay crude oil on the number and types of circulating hemocytes, on the phagocytic response, on spawning progression, and on internal structural changes. The number of hemocytes was reduced with 4-5 week exposure to 1000 nL/L of oil; a significant number of individuals showed a higher than average cell count with longer exposure. An increase in agranulocytes in the 8-9 week control population does not occur in populations exposed to 1000 nL/L and 500 nL/L of oil for 8-9 weeks, but, the phagocytic response was significantly depressed. The Chi-square test showed that oil interferes significantly with progression of spawning. Analysis of internal tissue structure indicates that oil can affect adipogranular storage cells, vesicular tissue, and digestive tubule cells. The changes occurring in circulating hemocytes are not necessarily consistent with changes in internal morphology.
    • Heterogeneity and bias in abundance estimates of outmigrating chinook salmon in the Chena River, Alaska

      Lambert, Ted M. (1998-12)
      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, α=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.
    • 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>
    • Hotspots and behavioral patterns of southern Alaska resident killer whales (Orcinus orca)

      Olsen, Daniel W.; Atkinson, Shannon; Mueter, Franz; Matkin, Craig (2017-05)
      The resident killer whale (Orcinus orca) is a genetically and behaviorally distinct ecotype of killer whale that feeds primarily on Pacific salmon (Oncorhynchus spp.). Long-term monitoring over 30 years of study has enabled detailed investigation into pod-specific, seasonal, and compositional differences in space use and behavior. To investigate use of habitat, 33 resident killer whales representing 14 pods in the northern Gulf of Alaska were tagged with satellite transmitters during all years from 2006 to 2014, and transmissions were received during the months of June to January. Core use areas were identified through utilization distributions using a biased Brownian Bridge movement model. Tagging results indicate different core use areas between pods, which could be due to cultural transmission within matrilineal groups. To investigate differences in behavior, 1337 hours of behavioral data were collected from 2006 to 2015. For these observations, chi squared tests were used to determine significant differences in behavior budgets between seasons, regions, haplotypes, and numbers of pods. The presence of 'rarely sighted' pods (sighted in less than 5% of encounters) had a large influence on the frequency of social behavior, which increased from 18.5% without their presence to 31.4% with it (X² = 17.3, df = 1, P < 0.001). Frequency of social behavior was also significantly affected by the number of pods present (X² = 72.8, df = 3,P < 0.001), and increased from 4.7% to 31.2% with one pod to more than four pods present. Strong seasonal and pod-specific differences were found in core use areas, possibly driven by the availability of seasonal salmon migration. Social behavior, and to some extent foraging and resting behaviors, appear to be driven by group composition and numbers of pods throughout the spring to fall seasons. Overall, these findings help clarify spatial and behavioral patterns observed for resident killer whales.
    • Humpback whale (Megaptera novaeangliae) entanglement in fishing gear in northern southeastern Alaska

      Neilson, Janet L. (2006-05)
      The prevalence of non-lethal entanglements of humpback whales (Megaptera novaeangliae) in fishing gear in northern southeastern Alaska (SEAK) was quantified using a scar-based method. The percentage of whales assessed to have been entangled ranged from 52% (minimal estimate) to 71% (conditional estimate) to 78% (maximal estimate). The conditional estimate is recommended because it is based solely on unambiguous scars. Eight percent of the whales in Glacier Bay/Icy Strait acquired new entanglement scars between years, although the sample size was small. Calves were less likely to have entanglement scars than older whales and males may be at higher risk than females. The temporal and spatial distribution of commercial fisheries is complex and difficult to correlate with these results. The percentage of whales with entanglement scarring is comparable to the Gulf of Maine where entanglement is a substantial management concern. Consequently, SEAK humpback whale-fisheries interactions may warrant a similar level of scrutiny.
    • Humpback whale habitat use patterns and interactions with vessels at Point Adolphus, Southeastern Alaska

      Koehler, Nicole (2006-12)
      Humpback whales at Point Adolphus, in southeastern Alaska, are faced with the challenge of maximizing their energy gain from feeding and minimizing energy losses that can occur due to disturbance by vessel traffic. Point Adolphus is unique because of abundant prey resources that attract high concentrations of humpback whales during the summer and high levels of vessel activity. Using scan sampling and focal behavior observation sessions data were collected from an elevated shore station on the northern coast of Chichagof Island in 2001. Humpback whale numbers peaked during early ebb tide. Whales were distributed west during ebbing tides and east during flooding tides. During flood tides, humpback whales exhibited non-directional movement. Differences in humpback whale numbers, distribution and movement patterns in relation to tide appeared related to small-scale fronts and headland wake effects associated with Point Adolphus. Overall, humpback whale swimming speeds were faster when the number of vessels present was greater and distance to the nearest vessel was smaller. However, responses of individual whales differed. Humpback whales at Point Adolphus appear to have developed strategies to exploit predictable times to feed which are tidally-induced and practice short-term avoidance strategies that may reduce the effects of vessel traffic.
    • Humpback whales and humans: a multi-disciplinary approach to exploring the whale-watching industry in Juneau, Alaska

      Teerlink, Suzanne F.; Horstmann, Larissa; Witteveen, Briana; Mueter, Franz; DeMaster, Doug; Beaudreau, Anne (2017-05)
      A booming whale-watching industry in Juneau, Alaska is leading to complicated resource management challenges. Juneau's growing commercial whale-watching industry includes over 60 vessels and generates more than $25 million in annual revenue. As this industry has increased, so too have concerns for the welfare of humpback whales (Megaptera novaeangliae) exposed to this vessel traffic. However, we lack a fundamental understanding of long-term impacts, if any, that vessel disturbance has on humpback whales. Further, we have insufficient data on local abundance and seasonal attendance of humpback whales that are necessary to detect potential future changes. The aim of this project is to investigate Juneau area humpback whales and their interactions with whale-watching tourism to set a foundation for sustainable management of this resource and industry. To reach this objective, three studies were employed. 1) Methods for monitoring humpback whale population parameters through a citizen science program were developed and tested. Photo-identification data were collected on whale-watching platforms and compared to data from dedicated surveys to objectively evaluate the citizen science data collection methods and identify biases. 2) Physiological markers were evaluated for signs of a chronic stress response in blubber of Juneau-area humpback whales compared with humpback whales from other areas in Alaska with far less vessel traffic. The concentrations of several steroid hormones, including cortisol, were measured from biopsy samples and used to infer a relative cumulative stress response in whales exposed to Juneau's tourism fleet. 3) Community perceptions toward Juneau's whale-watching industry and humpback whale management were collated to consider stakeholder concerns and suggestions for local humpback whale management. Participants were given the opportunity to share their perspectives on humpback whale welfare, community considerations and concerns, and recent and proposed management changes that affect the whale-watching industry. I found that citizen science data can produce reliable estimates of abundance, especially with sufficient effort. I did not find evidence for increased stress response in Juneau-area humpback whales and argue that this indicates habituation in these animals. Respondents in our survey generally supported Juneau's whale-watching industry, but expressed concerns for the vessel crowding and the welfare of humpback whales in this area. This project combines multiple scientific disciplines to tackle the initial steps necessary in understanding the complex interaction between humans and humpback whales near Juneau, and in making management decisions that ensure a sustainable future for Juneau's humpback whales and the whale-watching industry that relies on them.
    • Idealized Modeling Of Circulation Under Landfast Ice

      Kasper, Jeremy Lucas; Weingartner, Thomas; Gradinger, Rolf; Hedstrom, Katherine; Johnson, Mark; Kowalik, Zygmunt (2010)
      Idealized analytical and numerical models are used to elucidate the effects of a spatially variable landfast ice cover on under-ice circulation. Three separate forcing mechanisms are investigated; lateral inflow onto an ice-covered shelf (an elevated sea level at the western boundary), a spatially uniform upwelling wind blowing along the seaward landfast ice edge and a buoyant inflow under the ice cover that enters the domain through the southern coastal wall. The idealized models are configured to resemble the shallow Alaskan Beaufort Sea shelf. Models show that the inclusion of landfast ice means shelf response is substantially different from an ice-free shelf. In the case of a lateral inflow, landfast ice spreads the inflow offshore (in a manner similar to bottom friction) but the change in surface stress across the ice edge (from ice-covered to ice-free) limits the offshore spreading. In the case of an upwelling wind along the ice edge, the low sea level at the ice edge (due to ice edge upwelling) leads to a cross-shore sea level slope between the coast (high sea level) and the ice edge (low sea level), which drives a geostrophically balanced flow upwind. In the absence of along-shore changes in wind or ice the circulation does not vary along the shelf and currents near the coast are O(10 -3) m s-1. Along- and cross-shore variations in the ice-ocean friction coefficient introduce differences in the response time of the under-ice flow and can lead to along-shore sea level slopes, which drive along-shore flows near the coast (< 0.06 m s-1). In the case of a time dependent buoyant inflow, the landfast ice spreads the buoyant inflow much farther offshore (~ 9 times the local baroclinic Rossby radius, ~ 45 km) than in the ice-free case (< 30 km). When the ice width is finite, the change in surface across the ice edge acts to restrict offshore flow (in the anti-cyclonic bulge) and inhibits onshore flow farther downstream.
    • Idealized Modeling Of Seasonal Variation In The Alaska Coastal Current

      Williams, William James; Weingartner, Thomas (2003)
      Analytical and idealized-numerical models were used to understand the physical processes that govern the seasonal variation and fate of the freshwater in the Alaska Coastal Current (ACC). The ACC is forced by freshwater inflow and by mean easterly winds that cause downwelling over the shelf. Two-dimensional modeling using a line-source buoyant inflow gives the coastal current depth <math> <f> H=<fr><nu>3<sup>2/3</sup></nu><de>2</de></fr><fen lp="par"><fr><nu> f<sup>2</sup>Q<sup>2</sup></nu><de>g<sup>'</sup></de></fr> <rp post="par"></fen>t<sup>2/3</sup></f> </math> and coastal current width <math> <f> Y<inf>2D</inf>=3<sup>1/3</sup><fen lp="par"><fr><nu>g<sup>' </sup>Q</nu><de>f<sup>2</sup></de></fr><rp post="par"></fen><sup> 1/3</sup>t<sup>1/3</sup></f> </math>, where f is the Coriolis frequency, g ' is reduced gravity, Q is inflow rate and t is time since inflow began. Addition of downwelling wind-stress causes a steep coastal current front that intersects the bottom and is either convecting, stable and steady, or stable and oscillatory depending on <math> <f> <fr><nu>D</nu><de><g>d</g><inf>*</inf></de></fr></f> </math> and <math> <f> <fr><nu>b<inf>y</inf></nu><de>f<sup>2</sup></de></fr></f> </math>, where D is bottom depth, delta* is an Ekman depth and by is the cross-shelf buoyancy gradient. Three-dimensional modeling of a half-line source initially develops two-dimensionally but becomes three-dimensional from a balance between coastal influx of buoyancy and its downstream transport. This balance results in a coastal current depth limit <math> <f> H<inf><rf>max</rf></inf>=<fen lp="par"><fr><nu>2Qf</nu><de>g<sup> '</sup></de></fr><rp post="par"></fen><sup>1/2</sup>x<sup> 1/2</sup></f> </math>, where x is along-shelf distance. This limit is unchanged under downwelling wind-stress and is reached on time scales of less than 1 month for the ACC. The half-line source coastal current width develops as <math> <f> Y<inf>2D</inf></f> </math> away from the beginning of the line source. Imposition of a downwelling wind-stress tau results in an approximate balance among wind-stress and along- and cross-shelf momentum advection so that the current width is reduced to <math> <f> Y<inf>wind</inf>&ap;L<inf>D</inf><fen lp="par"><fr><nu>Qf</nu> <de><g>t</g>/<g>r</g><inf>0</inf></de></fr><rp post="par"></fen><sup> 1/2</sup></f> </math>, where LD is the Rossby radius of deformation. Waves and eddying motions eventually grow in the half-line source coastal current with wavelengths proportional to the coastal current width and with a downstream phase speed slower than the maximum current speed. These features cause an offshore flux of buoyant water, a broader coastal current and accumulation of buoyancy on the shelf. Increasing downwelling wind stress reduces the effects of the instabilities. Although buoyancy accumulates on the shelf during most model runs, there is little accumulation under maximum winter downwelling wind-stress. This suggests that freshwater accumulates on the shelf from spring through fall, but is then transported downstream during winter.
    • Identification and application of molecular markers to chum salmon population genetics

      Garvin, Michael R.; Gharrett, A. J.; Tallmon, David; Smoker, William (2008-08)
      I developed a new technique, DEco-TILLING (an adaptation of Eco-TILLING), to discover useful single nucleotide polymorphisms (SNPs) rapidly and inexpensively. Some chum salmon (Oncorhynchus keta) populations have declined in Western Alaska and in other areas of their geographic range. Possible reasons include climate shifts, by- catch in fisheries, and other perturbations. Genetics offers powerful tools that can be used to monitor this species on the high seas in stock mixtures aiding management of by- catch identification and other contributors to declines. Single nucleotide polymorphisms are a genetic marker that can be easily and rapidly surveyed on many individuals. Tools like SNPs offer advantages in discriminating stocks in mixtures. However, tens or hundreds of informative SNPs must be discovered from among the millions in the chum salmon genome. Available discovery methods introduce ascertainment bias into this process, which can result in uninformative SNPs or the failure to identify useful ones. I incorporated and improved a genotyping assay to screen SNPs in thousands of individuals for a tenth of the cost of the standard available assay, and improved an assay to resolve the phase of linked SNPs. I show that the SNPs that I discovered are informative and can be use for mixed stock analysis.
    • Identification and characterization of inconnu spawning habitat in the Sulukna River, Alaska

      Gerken, Jonathon D.; Margraf, Joseph; Zimmerman, Christian; Verbyla, David; Brown, Randy (2009-12)
      Inconnu (Stenodus leucichthys) is present throughout much of the Yukon River drainage in Alaska, but only five spawning areas have been identified. Spawning habitat requirements are therefore thought to be very specific; however, the physical qualities of these habitats have only been characterized in general terms. The Sulukna River is one of five identified inconnu spawning areas within the Yukon River drainage. A systematic sampling design was used in September and October of 2007-2008 to define Sulukna River spawning locations. Presence of inconnu was identified using hook and line sampling methods and spawning was verified by catching broadcast eggs in plankton nets. Small-scale, large-scale, and chemical habitat variables were sampled at transects located every 1.8 river kilometer (rkm). Project results indicate that spawning habitat was confined to a narrow reach of approximately 20 rkm. Spawning habitat occurred significantly more often in transects characterized with substrate between 6 and 12 cm, a width to depth ratio between 15 - 36, and water conductivity between 266 - 298 microsiemens per centimeter. Similar studies on other known spawning habitats would reveal whether these qualities are common to all inconnu spawning populations or unique to the Sulukna River.