Near-shore wave power characterized with a remotely controlled surface vehicle in Admiralty Inlet, Puget Sound, WA

Senior thesis written for Oceanography 445

An interview-based cognitive analysis of stakeholder perceptions of whale watching in Puget Sound, Washington

Thesis (Master's)--University of Washington, 2016-06

Size-selective mortality and environmental factors affecting early marine growth during early marine life stages of sub-yearling Chinook salmon in Puget Sound, Washington

Thesis (Master's)--University of Washington, 2016-08

Migration and Residence Patterns of Salmonids in Puget Sound, Washington

Thesis (Ph.D.)--University of Washington, 2016-08

Mapping Whidbey Island and Possession Sound landslide susceptibility using an additive linear model

Senior thesis written for Oceanography 445

MARS (Media Asset Retrieval System): Puget Sound’s Digital Archive

The MARS (Media Asset Retrieval System) Project is the collaborative effort of public broadcasters,libraries and schools in the Puget Sound region to create a digital online resource that provides access to content produced by public broadcasters via the public libraries. Convergence ConsortiumThe Convergence Consortium is a model for community collaboration, including organizations such as public broadcasters, libraries, museums, and schools in the Puget Sound region to assess the needs of their constituents and pool resources to develop solutions to meet those needs. Specifically, the archives of public broadcasters have been identified as significant resources for the local communities and nationally. These resources can be accessed on the broadcasters websites, and through libraries and used by schools, and integrated with text and photographic archives from other partners.MARS’ goalCreate an online resource that provides effective access to the content produced locally by KCTS (Seattle PBS affiliate) and KUOW (Seattle NPR affiliate). The broadcasts will be made searchable using the CPB Metadata Element Set (under development) and controlled vocabularies (to be developed). This will ensure a user friendly search and navigation mechanism and user satisfaction.Furthermore, the resource can search the local public library’s catalog concurrently and provide the user with relevant TV material, radio material, and books on a given subject.The ultimate goal is to produce a model that can be used in cities around the country.The current phase of the project assesses the community’s need, analyzes the current operational systems, and makes recommendations for the design of the resource.Deliverables• Literature review of the issues surrounding the organization, description and representation of media assets• Needs assessment report of internal and external stakeholders• Profile of the systems in the area of managing and organizing media assetsfor public broadcasting nationwideActivities• Analysis of information seeking behavior• Analysis of collaboration within the respective organizations• Analysis of the scope and context of the proposed system• Examining the availability of information resources and exchangeof resources among users

Puget Sound’s MARS (Media Asset Retrieval System) Digital Library

The MARS (Media Asset Retrieval System) Project is a collaboration between public broadcasters, libraries and schools in the Puget Sound region to assess the needs of their constituents and pool resources to develop solutions to meet those needs. The Project’s ultimate goal is to create a digital online resource that will provide access to content produced by public broadcasters and libraries. The MARS Project is funded by a grant from the Corporation for Public Broadcasting (CPB) Television Future Fund. Convergence ConsortiumThe Convergence Consortium is a model for community collaboration, including representatives from public broadcasting, libraries and schools in the Puget Sound region. They meet regularly to consider collaborative efforts that will be mutually beneficial to their institutions and constituents. Specifically, the archives of public broadcasters have been identified as significant resources that can be accessed through libraries and used by schools, and integrated with text and photographic archives from other partners.Using the work-centered framework, we collected data through interviews with nine engineers and observation of their searching while they performed their regular, job-related searches on the Web. The framework was used to analyze the data on two levels: 1) the activities and organizational relationships and constrains of work domains, and 2) users’ cognitive and social activities and their subjective preferences during searching.

Ecological condition of coastal ocean waters along the U.S. Western Continental Shelf: 2003

Executive Summary: The western National Coastal Assessment (NCA-West) program of EPA, in conjunction with the NOAA National Ocean Service (NOS), conducted an assessment of the status of ecological condition of soft sediment habitats and overlying waters along the western U.S. continental shelf, between the target depths of 30 and 120 m, during June 2003. NCA-West and NOAA/NOS partnered with the West Coast states (Washington (WA), Oregon (OR), and California (CA)), and the Southern California Coastal Water Research Project (SCCWRP) Bight ’03 program to conduct the survey. A total of 257 stations were sampled from Cape Flattery, WA to the Mexican border using standard methods and indicators applied in previous coastal NCA projects. A key study feature was the incorporation of a stratified-random sampling design with stations stratified by state and National Marine Sanctuary (NMS) status. Each of the three states was represented by at least 50 random stations. There also were a total of 84 random stations located within NOAA’s five NMSs along the West Coast including the Olympic Coast NMS (OCNMS), Cordell Bank NMS (CBNMS), Gulf of Farallones NMS (GFNMS), Monterey Bay NMS (MBNMS), and Channel Islands NMS (CINMS). Collection of flatfish via hook-and-line for fish-tissue contaminant analysis was successful at 50 EMAP/NCA-West stations. Through a collaboration developed with the FRAM Division of the Northwest Fisheries Science Center, fish from an additional 63 stations in the same region and depth range were also analyzed for fish-tissue contaminants. Bottom depth throughout the region ranged from 28 m to 125 m for most stations. Two slightly deeper stations from the Southern California Bight (SCB) (131, 134 m) were included in the data set. About 44% of the survey area had sediments composed of sands (< 20% silt-clay), about 47% was composed of intermediate muddy sands (20-80% silt-clay), and about 9% was composed of muds (> 80% silt-clay). The majority of the survey area (97%) had relatively low percent total organic carbon (TOC) levels of < 2%, while a small portion (< 1%) had high TOC levels (> 5%), in a range potentially harmful to benthic fauna. Salinity of surface waters for 92% of the survey area were > 31 psu, with most stations < 31 psu associated with the Columbia River plume. Bottom salinities ranged only between 31.6 and 34.4 psu. There was virtually no difference in mean bottom salinities among states or between NMS and non-NMS stations. Temperatures of surface water (range 8.5 -19.9 °C) and bottom water (range 5.8 -14.7 °C) averaged several degrees higher in CA in comparison to WA and OR. The Δσt index of watercolumn stratification indicated that about 31% of the survey area had strong vertical stratification of the water column. The index was greatest for waters off WA and lowest for CA waters. Only about 2.6 % of the survey area had surface dissolved oxygen (DO) concentrations ≤ 4.8 mg/L, and there were no values below the lower threshold (2.3 mg/L) considered harmful to the survival and growth of marine animals. Surface DO concentrations were higher in WA and OR waters than in CA, and higher in the OC NMS than in the CA sanctuaries. An estimated 94.3% of the area had bottom-water DO concentrations ≤ 4.8 mg/L and 6.6% had concentrations ≤ 2.3 mg/L. The high prevalence of DO from 2.3 to 4.8 mg/L (85% of survey area) is believed to be associated with the upwelling of naturally low DO water across the West Coast shelf. Mean TSS and transmissivity in surface waters (excluding OR due to sample problems) were slightly higher and lower, respectively, for stations in WA than for those in CA. There was little difference in mean TSS or transmissivity between NMS and non-NMS locations. Mean transmissivity in bottom waters, though higher in comparison to surface waters, showed little difference among geographic regions or between NMS and non-NMS locations. Concentrations of nitrate + nitrite, ammonium, total dissolved inorganic nitrogen (DIN) and orthophosphate (P) in surface waters tended to be highest in CA compared to WA and OR, and higher in the CA NMS stations compared to CA non-sanctuary stations. Measurements of silicate in surface waters were limited to WA and CA (exclusive of the SCB) and showed that concentrations were similar between the two states and approximately twice as high in CA sanctuaries compared to OCNMS or nonsanctuary locations in either state. The elevated nutrient concentrations observed at CA NMS stations are consistent with the presence of strong upwelling at these sites at the time of sampling. Approximately 93% of the area had DIN/P values ≤ 16, indicative of nitrogen limitation. Mean DIN/P ratios were similar among the three states, although the mean for the OCNMS was less than half that of the CA sanctuaries or nonsanctuary locations. Concentrations of chlorophyll a in surface waters ranged from 0 to 28 μg L-1, with 50% of the area having values < 3.9 μg L-1 and 10% having values > 14.5 μg L-1. The mean concentration of chlorophyll a for CA was less than half that of WA and OR locations, and concentrations were lowest in non-sanctuary sites in CA and highest at the OCNMS. Shelf sediments throughout the survey area were relatively uncontaminated with the exception of a group of stations within the SCB. Overall, about 99% of the total survey area was rated in good condition (<5 chemicals measured above corresponding effect range low (ERL) concentrations). Only the pesticides 4,4′-DDE and total DDT exceeded corresponding effect range-median (ERM) values, all at stations in CA near Los Angeles. Ten other contaminants including seven metals (As, Cd, Cr, Cu, Hg, Ag, Zn), 2-methylnaphthalene, low molecular weight PAHs, and total PCBs exceeded corresponding ERLs. The most prevalent in terms of area were chromium (31%), arsenic (8%), 2-methylnaphthalene (6%), cadmium (5%), and mercury (4%). The chromium contamination may be related to natural background sources common to the region. The 2-methylnaphthalene exceedances were conspicuously grouped around the CINMS. The mercury exceedances were all at non-sanctuary sites in CA, particularly in the Los Angeles area. Concentrations of cadmium in fish tissues exceeded the lower end of EPA’s non-cancer, human-health-risk range at nine of 50 EMAP/NCA-West and nine of 60 FRAM groundfish-survey stations, including a total of seven NMS stations in CA and two in the OCNMS. The human-health guidelines for all other contaminants were only exceeded for total PCBs at one station located in WA near the mouth of the Columbia River. Benthic species richness was relatively high in these offshore assemblages, ranging from 19 to 190 taxa per 0.1-m2 grab and averaging 79 taxa/grab. The high species richness was reflected over large areas of the shelf and was nearly three times greater than levels observed in estuarine samples along the West Coast (e.g NCA-West estuarine mean of 26 taxa/grab). Mean species richness was highest off CA (94 taxa/grab) and lower in OR and WA (55 and 56 taxa/grab, respectively). Mean species richness was very similar between sanctuary vs. non-sanctuary stations for both the CA and OR/WA regions. Mean diversity index H′ was highest in CA (5.36) and lowest in WA (4.27). There were no major differences in mean H′ between sanctuary vs. nonsanctuary stations for both the CA and OR/WA regions. A total of 1,482 taxa (1,108 to species) and 99,135 individuals were identified region-wide. Polychaetes, crustaceans and molluscs were the dominant taxa, both by percent abundance (59%, 17%, 12% respectively) and percent species (44%, 25%, 17%, respectively). There were no major differences in the percent composition of benthic communities among states or between NMSs and corresponding non-sanctuary sites. Densities averaged 3,788 m-2, about 30% of the average density for West Coast estuaries. Mean density of benthic fauna in the present offshore survey, averaged by state, was highest in CA (4,351 m-2) and lowest in OR (2,310 m-2). Mean densities were slightly higher at NMS stations vs. non-sanctuary stations for both the CA and OR/WA regions. The 10 most abundant taxa were the polychaetes Mediomastus spp., Magelona longicornis, Spiophanes berkeleyorum, Spiophanes bombyx, Spiophanes duplex, and Prionospio jubata; the bivalve Axinopsida serricata, the ophiuroid Amphiodia urtica, the decapod Pinnixa occidentalis, and the ostracod Euphilomedes carcharodonta. Mediomastus spp. and A. serricata were the two most abundant taxa overall. Although many of these taxa have broad geographic distributions throughout the region, the same species were not ranked among the 10 most abundant taxa consistently across states. The closest similarities among states were between OR and WA. At least half of the 10 most abundant taxa in NMSs were also dominant in corresponding nonsanctuary waters. Many of the abundant benthic species have wide latitudinal distributions along the West Coast shelf, with some species ranging from southern CA into the Gulf of Alaska or even the Aleutians. Of the 39 taxa on the list of 50 most abundant taxa that could be identified to species level, 85% have been reported at least once from estuaries of CA, OR, or WA exclusive of Puget Sound. Such broad latitudinal and estuarine distributions are suggestive of wide habitat tolerances. Thirteen (1.2%) of the 1,108 identified species are nonindigenous, with another 121 species classified as cryptogenic (of uncertain origin), and 208 species unclassified with respect to potential invasiveness. Despite uncertainties of classification, the number and densities of nonindigenous species appear to be much lower on the shelf than in the estuarine ecosystems of the Pacific Coast. Spionid polychaetes and the ampharetid polychaete Anobothrus gracilis were a major component of the nonindigenous species collected on the shelf. NOAA’s five NMSs along the West Coast of the U.S. appeared to be in good ecological condition, based on the measured indicators, with no evidence of major anthropogenic impacts or unusual environmental qualities compared to nearby nonsanctuary waters. Benthic communities in sanctuaries resembled those in corresponding non-sanctuary waters, with similarly high levels of species richness and diversity and low incidence of nonindigenous species. Most oceanographic features were also similar between sanctuary and non-sanctuary locations. Exceptions (e.g., higher concentrations of some nutrients in sanctuaries along the CA coast) appeared to be attributable to natural upwelling events in the area at the time of sampling. In addition, sediments within the sanctuaries were relatively uncontaminated, with none of the samples having any measured chemical in excess of ERM values. The ERL value for chromium was exceeded in sediments at the OCNMS, but at a much lower percentage of stations (four of 30) compared to WA and OR non-sanctuary areas (31 of 70 stations). ERL values were exceeded for arsenic, cadmium, chromium, 2- methylnaphthalene, low molecular weight PAHs, total DDT, and 4,4′-DDE at multiple sites within the CINMS. However, cases where total DDT, 4,4′-DDE, and chromium exceeded the ERL values were notably less prevalent at CINMS than in non-sanctuary waters of CA. In contrast, 2-methylnaphthalene above the ERL was much more prevalent in sediments at the CINMS compared to non-sanctuary waters off the coast of CA. While there are natural background sources of PAHs from oil seeps throughout the SCB, this does not explain the higher incidence of 2-methylnaphthalene contamination around CINMS. Two stations in CINMS also had levels of TOC (> 5%) potentially harmful to benthic fauna, though none of these sites exhibited symptoms of impaired benthic condition. This study showed no major evidence of extensive biological impacts linked to measured stressors. There were only two stations, both in CA, where low numbers of benthic species, diversity, or total faunal abundance co-occurred with high sediment contamination or low DO in bottom water. Such general lack of concordance suggests that these offshore waters are currently in good condition, with the lower-end values of the various biological attributes representing parts of a normal reference range controlled by natural factors. Results of multiple linear regression, performed using full model procedures to test for effects of combined abiotic environmental factors, suggested that latitude and depth had significant influences on benthic variables regionwide. Latitude had a significant inverse influence on all three of the above benthic variables, i.e. with values increasing as latitude decreased (p< 0.01), while depth had a significant direct influence on diversity (p < 0.001) and inverse effect on density (p <0.01). None of these variables varied significantly in relation to sediment % fines (at p< 0.1), although in general there was a tendency for muddier sediments (higher % fines) to have lower species richness and diversity and higher densities than coarser sediments. Alternatively, it is possible that for some of these sites the lower values of benthic variables reflect symptoms of disturbance induced by other unmeasured stressors. The indicators in this study included measures of stressors (e.g., chemical contaminants, eutrophication) that are often associated with adverse biological impacts in shallower estuarine and inland ecosystems. However, there may be other sources of humaninduced stress in these offshore systems (e.g., bottom trawling) that pose greater risks to ambient living resources and which have not been captured. Future monitoring efforts in these offshore areas should include indicators of such alternative sources of disturbance. (137pp.) (PDF contains 167 pages)

Distribution and Abundance of Juvenile Salmonids off Oregon and Washington, 1981-1985

This report is a summary of the results of 883 purse seine sets made for juvenile salmonids during 15 cruises off the coasts of Oregon and Washington during the springs and summers of 1981-1985. Juvenile coho salmon (Oncorhynchus kisutch) occurred most frequently, followed by chinook salmon (0. tshawytscha). The juveniles of these two species co-occurred more frequently than expected. Juvenile chum, pink and sockeye salmon (0. keta, O. gorbuscha, and O. nerka), steelhead (0. mykiss) and cutthroat trout (0. clarki clarki) were caught much less frequently and in lower numbers than coho or chinook salmon. We found no evidence of large schools ofjuvenile salmonids. A northerly movement of juvenile coho salmon wa~ suggested by decreased catches off Oregon and increased catches off Washington between early and late summer. Highest catch per set of juvenile coho salmon was usually found inshore of 37.2 km. Juvenile chinook salmon were usually found within 27.9 km of the coast. Juvenile salmonids were found over a broad range of surface salinities and temperatures. High catches of juvenile coho salmon occurred in both the low salinity waters of the Columbia River plume and in adjacent higher salinity waters. Preferences for specific salinities or temperatures were not obvious for any species, although catch rates of juvenile coho salmon were highest in years when chlorophyll content was also high. Based on expansions of fish with coded wire tags, we estimated that hatchery coho salmon smolts comprised 74%, on average, of the juvenile coho salmon catches. The remaining 26% were presumably wild fish or hatchery fish released as fingerlings. Hatchery coho salmon were caught roughly in proportion to the numbers released. However, hatchery fish from the Columbia River and private coastal facilities were caught at slightly higher rates while those from coastal Washington and public coastal Oregon hatcheries were caught at slightly lower rates than expected from the numbers released. No juvenile coho salmon with coded wire tags were caught that had originated from either California or Puget Sound hatcheries. (PDF file contains 88 pages.)

Developing alternative shoreline armoring strategies: the living shoreline approach in North Carolina

This paper reviews the scientific data on the ecosystem services provided by shoreline habitats, the evidence for adverse impacts from bulkheading on those habitats and services, and describes alternative approaches to shoreline stabilization, which minimize adverse impacts to the shoreline ecosystem. Alternative shoreline stabilization structures that incorporate natural habitats, also known as living shorelines, have been popularized by environmental groups and state regulatory agencies in the mid-Atlantic. Recent data on living shoreline projects in North Carolina that include a stone sill demonstrate that the sills increase sedimentation rates, that after 3 years marshes behind the sills have slightly reduced biomass, and that the living shoreline projects exhibit similar rates of fishery utilization as nearby natural fringing marshes. Although the current emphasis on shoreline armoring in Puget Sound is on steeper, higher-energy shorelines, armoring of lower-energy shorelines may become an issue in the future with expansion of residential development and projected rates of sea level rise. The implementation of regulatory policy on estuarine shoreline stabilization in North Carolina and elsewhere is presented. The regulatory and public education issues experienced in North Carolina, which have made changes in estuarine shoreline stabilization policy difficult, may inform efforts to adopt a sustainable shoreline armoring strategy in Puget Sound. A necessary foundation for regulatory change in shoreline armoring policy, and public support for that change, is rigorous scientific assessment of the variety of services that natural shoreline habitats provide both to the ecosystem and to coastal communities, and evidence demonstrating that shoreline armoring can adversely impact the provision of those services.

Genetic analysis of juvenile coho salmon (Oncorhynchus kisutch) off Oregon and Washington reveals few Columbia River wild fish

Little is known about the ocean distributions of wild juvenile coho salmon off the Oregon-Washington coast. In this study we report tag recoveries and genetic mixed-stock estimates of juvenile fish caught in coastal waters near the Columbia River plume. To support the genetic estimates, we report an allozyme-frequency baseline for 89 wild and hatchery-reared coho salmon spawning populations, extending from northern California to southern British Columbia. The products of 59 allozyme-encoding loci were examined with starch-gel electrophoresis. Of these, 56 loci were polymorphic, and 29 loci had P0.95 levels of polymorphism. Average heterozygosities within populations ranged from 0.021 to 0.046 and averaged 0.033. Multidimensional scaling of chord genetic distances between samples resolved nine regional groups that were sufficiently distinct for genetic mixed-stock analysis. About 2.9% of the total gene diversity was due to differences among populations within these regions, and 2.6% was due to differences among the nine regions. This allele-frequency data base was used to estimate the stock proportions of 730 juvenile coho salmon in offshore samples collected from central Oregon to northern Washington in June and September-October 1998−2000. Genetic mixed-stock analysis, together with recoveries of tagged or fin-clipped fish, indicates that about one half of the juveniles came from Columbia River hatcheries. Only 22% of the ocean-caught juveniles were wild fish, originating largely from coastal Oregon and Washington rivers (about 20%). Unlike previous studies of tagged juveniles, both tag recoveries and genetic estimates indicate the presence of fish from British Columbia and Puget Sound in southern waters. The most salient feature of genetic mixed stock estimates was the paucity of wild juveniles from natural populations in the Columbia River Basin. This result reflects the large decrease in the abundances of these populations in the last few decades.

Tidal Energy Resource Characterization in Alberni Inlet, B.C.

Senior thesis written for Oceanography 444

The effect of shore armoring on beach slope in mixed sand-and-gravel beaches

Senior thesis written for Oceanography 445

Analyzing drifter designs and data gathering methods in complex estuarine environments

Senior thesis written for Oceanography 445

Growing biofuel outdoors in Seattle: effects of natural light level and temperature on marine microalgal culture density and lipid content in contained natural exposure systems

Senior thesis written for Oceanography 445