The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012

As competing uses of our coastlines increase, natural resource agencies are employing marine spatial planning (MSP) to designate areas for different uses or activities in order to reduce conflicts while achieving ecological, economic and social objectives. A central challenge of implementing MSP is development of a rigorous approach for analyzing tradeoffs across the provision of ecosystem services (i.e., the benefits humans receive from nature). This study develops an operational approach to this problem that is founded on community-based methods, ecological production theory, and multi-criteria decision analysis (MCDA). The approach merges ecological models with surveys to identify marine ecosystem services for use in tradeoff analysis. The approach allows for a single set of marine ecosystem services to at once be valued by local stakeholders and measured by biologists, thus connecting social and biological monitoring efforts. To develop the approach in a real-world context, I examined ecosystem services associated with nearshore marine ecosystems in Oregon, where marine reserves are being introduced for biodiversity conservation. I worked with stakeholder focus groups in three Oregon communities to identify 24 marine ecosystem services. I then linked the ecosystem services with ecological indicators, which I then consolidated to derive 11 items for use in a survey-based tradeoff analysis exercise. I administered the survey to a nonrandom sample of stakeholders in Oregon (n=31), from which their relative preferences and preference weights for ecosystem services were derived. The weights and preference measures may then be used in MSP decision-making. Furthermore, I grouped the stakeholder survey data in three ways: by location of residence (coastal vs. non-coastal), by eight categories of affiliation (e.g., business owners, conservationists, commercial and recreational fishers, etc.), and by resource use patterns. I then analyzed the various groupings of stakeholders for within- and between-group homogeneity of preferences. Results of the analyses showed that there are statistically significant variations in preferences within and between most groupings. Capturing the variations in stakeholder preferences is important when developing policies that affect different stakeholder groups. Thus, when implementing the survey instrument, I suggest random sampling of stakeholders stratified by location, affiliation, and resource use. This study provides one of the first examples of a systems-based approach to ecosystem service valuation operationalized to inform MSP, and novel features of the approach have a number of implications for advancing marine research and management. First, by using stakeholders to identify ecosystem services, the approach allows for a tailored implementation of ecosystem-based management at the community level. Second, by integrating ecological and economic information on the provision and value of ecosystem services, the approach provides relevant data for MSP decision-making during the siting, evaluation, and monitoring stages. And third, by applying both stated-preference and MCDA methods, the approach may capture the array of values represented by diverse stakeholder groups. / Graduation date: 2013

Variable ocean conditions can greatly impact lower trophic level prey assemblages in marine ecosystems, with effects propagating up to higher trophic levels. Our goal was to better understand how varying ocean conditions influence diets and niche overlap among a suite of low- to mid trophic level predators. We studied the diets of common murres (Uria aalge) over 10 contrasting years between 1998 and 2011, a period in which the Northern California Current experienced dramatic interannual variability in ocean conditions. Likewise, murre diets off Oregon varied considerably. Interannual variation in murre chick diets appears to be influenced by environmental drivers occurring before and during the breeding season, at both basin and local spatial scales. While clupeids were an important diet component throughout the study period, in some years murre diets were dominated by Pacific sand lance (Ammodytes hexapterus) and other years by osmerids (likely Allosmerus elongatus and Hypomesus pretiosus). Years in which the Pacific Decadal Oscillation and local sea surface temperatures were above average during summer months also showed elevated levels of clupeids in murre diets, while years with higher winter ichthyoplankton biomass and summer northern copepod biomass anomalies had fewer clupeids and more sand lance and smelts. Years with higher Northern Oscillation Index values during summer months also showed more smelts in the murre diets. Nesting phenology and reproductive success were correlated with diet as well, reflecting demographic consequences of environmental variability mediated through bottom-up food web dynamics. To examine niche overlap between murres and other marine predators we employed collaborative fisheries research with synoptic observations of a major seabird colony to determine the diets of four predator species on the central Oregon coast during two years of contrasting El Niño (2010) vs. La Niña (2011) conditions. The greatest degree of dietary overlap was observed between Chinook salmon (Oncorhynchus tshawytscha) and common murres, with both smelts (Osmeridae) and clupeids (primarily Clupea pallasii) observed as the dominant prey types. Diets differed between El Niño and La Niña conditions for two predators, murres and black rockfish (Sebastes melanops). During La Niña, smelts decreased, while sand lance increased in common murre diets. Black rockfish had fewer larval Dungeness crabs (Cancer magister) and a greater proportion of crab species associated with the later spring transition. Chinook salmon and Pacific halibut (Hippoglossus stenolepis) diets were similar during El Niño and La Niña conditions. These findings underscore that the diets of common murres during chick rearing reflect local- and basin-scale biophysical processes in the Northern California Current, and are valuable for understanding the response of upper trophic level organisms to changing oceanographic conditions. Additionally, using multiple predators across several diverse taxa to track changes in prey communities provided a way to detect seemingly subtle changes in prey communities and contributes to a more comprehensive understanding of food web dynamics and ecosystem indicators. / Graduation date: 2012

Nearshore hypoxia within the Northern California Current (NCC) system is a seasonal phenomenon caused by coastal upwelling and occurs mainly during late-summer and early fall. The effects of low oxygen levels on fish and invertebrate communities, particularly during early-life history stages, however, are poorly known for this area. I investigated the effects of hypoxia on the density, community structure, vertical and horizontal distribution of fish larvae and juveniles, as well as body condition of juveniles, along the central Oregon and Washington coasts during the summers of 2008 - 2011. During this sampling period, bottom dissolved oxygen (DO) values ranged from 0.49 to 9.85 ml l�����, and the number of hypoxic (e.g., < 1.4 ml l�����) stations sampled was low compared to 2002 and 2006 (only 54 sampling stations for the ichthyoplankton study out of 493, and only 12 stations out of 90 for the benthic juvenile study). From the ichthyoplankton study, I found that the overall density of fish larvae increased as bottom-DO values increased; however, the effect on individual species density was limited. Between 44.65 ��N and 46.00 ��N (~Florence, OR ��� Astoria, OR), fish larvae altered their vertical distribution when bottom-DO was low by rising in shallower water layers. From the benthic juvenile study, I found that English sole (Parophrys vetulus), butter sole (Isopsetta isolepis), speckled sanddab (Citharichthys stigmaeus) and Pacific sanddab (Citharichthys sordidus) dominated the catch with annual variation in abundances. Species composition, abundance and length had strong relationships with depth. Species abundance for English sole (< 75 mm), speckled sanddab (<100 mm) and Pacific sanddab also increased with increased bottom-DO. However, the body condition of butter sole (< 75 mm) and of large speckled sanddab (���100 mm) increased with decreased bottom-DO. Overall my research elucidates important patterns of larval and juvenile fish distribution within the NCC during summer. In both studies I have found a limited effect of DO on abundance, distribution and community assemblages. Variables other than DO, such as depth, season and location, dominated the explained variance of the intervening multivariate and univariate analysis. However, due to the paucity of samples during hypoxic events, continued monitoring of nearshore larval and juvenile species over varying hypoxic conditions is necessary for understanding the impact of hypoxia on these communities and subsequent adult populations. / Graduation date: 2013

The phylogenetic diversity of two continental shelf picoplankton communities was examined by analyzing SSU (16S) ribosomal RNA (rRNA) genes amplified from environmental DNA with bacterial-specific primers and the polymerase chain reaction (PCR). Picoplankton populations collected from the pycnocline (10 m) over the eastern continental shelf of the United States near Cape Hatteras, North Carolina, and surface seawater (10 m) from the western continental shelf of the United States 8 km west of Yaquina Head, Oregon, served as sources of bulk nucleic acids used in this study. A total of 285 SSU rRNA gene clones were analyzed in the two libraries, more than doubling the number previously available from seawater samples. In contrast to previous studies of bacterioplankton diversity from the open-ocean, a large proportion of the rDNA clones recovered in this study (38%) were related to plastid SSU rRNA genes, including plastids from bacillariophyte, prymnesiophyte, cryptophyte, chrysophyte, and prasinophyte algae, as well as a number of unique plastid rRNA gene clones for which no close phylogenetic relatives were discovered. A majority of the bacterial gene clones recovered (72% of bacterial clones) were closely related to rRNA gene lineages discovered previously in clone libraries from open-ocean marine habitats, including the SAR86 cluster (�� Proteobacteria), SAR83, SAR11, and SAR116 clusters (all �� Proteobacteria), the marine Gram-positive cluster (Actinomycetes), the marine group A/SAR406 cluster, and a cluster of environmental clones within the flexibacter-cytophaga-bacteroides phylum. A majority of the remaining bacterial clones were phylogenetically related to the �� and �� subclasses of the Proteobacteria, including an rDNA lineage within the Type I methylotroph Glade of the �� subclass. The abundance of plastid rDNAs and the lack of cyanobacterial-related clones, as well as the presence of �� Proteobacteria, are features of these coastal picoplankton gene clone libraries which distinguish them from similar studies of oligotrophic open-ocean sites. Overall, however, these data indicate that a limited number of as yet uncultured bacterioplankton lineages, related to those previously observed in the open-ocean, can account for the majority of cells in these coastal marine bacterioplankton assemblages. / Graduation date: 1998

Tsang, Ling Ming . / Thesis (M.Phil.)--Chinese University of Hong Kong, 2007. / Includes bibliographical references (leaves 84-104). / Abstracts in English and Chinese. / ABSTRACT --- p.i / ACKNOWLEDGEMENTS --- p.vi / CONTENTS --- p.viii / LIST OF TABLES --- p.xi / LIST OF FIGURES --- p.xii / Chapter Chapter 1 --- General Introduction --- p.1 / Chapter Chapter 2 --- Literature Review / Chapter 2.1 --- Molecular systematics --- p.6 / Chapter 2.2 --- Molecular markers as a tool for identification of cryptic species --- p.7 / Chapter 2.3 --- Molecular markers for delineating species and morphotypes --- p.10 / Chapter 2.4 --- Molecular markers for identification of hybrids --- p.12 / Chapter 2.5 --- Phylogeography of the marine biota through Pleistocene glaciations --- p.14 / Chapter Chapter 3 --- "Cryptic Diversity of the Acorn Barnacle, Tetraclita squamosa Species Complex in East Asia" / Chapter 3.1 --- Introduction --- p.18 / Chapter 3.2 --- Materials and methods --- p.20 / Chapter 3.2.1 --- Sample collection --- p.20 / Chapter 3.2.2 --- "DNA extraction, PCR and sequencing" --- p.20 / Chapter 3.2.3 --- Sequence analysis --- p.22 / Chapter 3.3 --- Results --- p.23 / Chapter 3.4 --- Discussion --- p.28 / Chapter 3.4.1 --- Genetic variations of Tetraclita squamosa --- p.28 / Chapter 3.4.2 --- Identification of new species --- p.31 / Chapter 3.4.3 --- Biogeography and distribution patterns --- p.32 / Chapter Chapter 4 --- "Lack of Genetic Differentiation among Acorn Barnacles Tetraclita japonica and Tetraclita formosana Populations in Mitochondrial COI, Control Region and Nuclear ITS1 Sequences" / Chapter 4.1 --- Introduction --- p.35 / Chapter 4.2 --- Materials and methods --- p.36 / Chapter 4.2.1 --- Samples collection --- p.36 / Chapter 4.2.2 --- "DNA extraction, PCR and DNA sequencing" --- p.38 / Chapter 4.2.3 --- Sequence analysis --- p.39 / Chapter 4.3 --- Results --- p.40 / Chapter 4.3.1 --- Genetic divergence --- p.40 / Chapter 4.3.2 --- Phylogenetic and population genetic analysis --- p.42 / Chapter 4.4 --- Discussion --- p.48 / Chapter 4.4.1 --- Molecular variation between Tetraclita japonica and T. formosana --- p.48 / Chapter 4.4.2 --- Population structure in East Asia --- p.49 / Chapter 4.4.3 --- Geographical variation in parietes color: environmental or genetic? --- p.50 / Chapter Chapter 5 --- Genetic Differentiation and Hybridization between T. japonica and T. formosana revealed by Amplified Fragments Length Polymorphism Analysis: Incipient Speciation in Glaciation Refugia? / Chapter 5.1 --- Introduction --- p.54 / Chapter 5.2 --- Materials and methods --- p.59 / Chapter 5.2.1 --- Sample collection --- p.59 / Chapter 5.2.2 --- AFLP analysis --- p.59 / Chapter 5.2.3 --- Statistical data analyses --- p.61 / Chapter 5.3 --- Results --- p.63 / Chapter 5.3.1 --- AFLP pattern and genetic diversity --- p.63 / Chapter 5.3.2 --- Genetic variation between the two species and among different populations --- p.63 / Chapter 5.3.3 --- Assessing population clustering by Bayesian analyses and admixture analyses --- p.67 / Chapter 5.4 --- Discussion --- p.71 / Chapter 5.4.1 --- Genetic differentiation and proposed subspecies designation --- p.71 / Chapter 5.4.2 --- Evolutionary history of the two species in relation to Pleistocene glaciation --- p.72 / Chapter 5.4.3 --- Hybridization between the two species and population structuring --- p.77 / Chapter Chapter 6 --- General Conclusions --- p.81 / References --- p.84

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The microsporidian parasite Nadelspora canceri infects Dungeness crabs, Cancer magister, along the United States Pacific Northwest coast. The prevalence and seasonal variation of N. canceri in Dungeness crabs from Alsea Bay, Oregon, are described based on examination of 2991 crabs collected at monthly intervals from October, 1991 to June, 1993. The average prevalence in monthly samples was 21.0% and ranged from 8.2% to 33.0%. No significant differences in monthly or seasonal parasite prevalence were observed. A total of 3061 Dungeness crabs was examined from an additional seven Pacific Northwest estuaries and Puget Sound to document the geographic distribution of N. canceri and the prevalence of the parasite in these locations. The estuaries sampled and the prevalences observed were: Humboldt Bay, California (14.6%), Coos Bay (10.6%), Yaquina Bay (2.0%), Tillamook Bay (41.2%), and Nehalem Bay, Oregon (14.2%), Willapa Bay (6.9%), and Grays Harbor Washington (0.44%). Dungeness crabs were examined from the Dungeness spit, Kala Point, and Mukilteo areas in Puget Sound and no infected crabs were found. A total of 9317 male Dungeness crabs > 15.9 cm carapace width (CW) captured in the commercial ocean crab fishery was examined for N. canceri and 27 (0.3%) were infected with the parasite. No infections were found in crabs smaller than 3.0 cm CW and the prevalence of infection generally increased with crab size reaching a peak of 22.2% in 14 cm CW crabs. The overall infection prevalence in male crabs (19.2%) was more than twice that of female crabs (8.0%), and of the 821 infected crabs found, 629 (76.6%) were males. The mortality of laboratory-held Dungeness crabs naturally infected with N. canceri was compared to that of uninfected crabs in two separate experiments and in both cases a significantly higher mortality was observed for infected crabs. Nadelspora canceri infections were established in both juvenile and adult Dungeness crabs that were fed parasite spores in laboratory experiments indicating that transmission is direct and intermediate hosts or vectors are not required for transmitting the parasite between hosts. / Graduation date: 1995

Graduation date: 1963

Graduation date: 2006 / Presented on 2005-12-02 / An empirical statistical model is developed that relates the non-tidal motion of the ocean surface currents off the Oregon coast to forecasts of the coastal winds. The empirical statistical model is then used to produce predictions of the surface currents that are evaluated for their agreement with measured currents. Measurements of the ocean surface currents were made at 6 km resolution using Long-Range CODAR SeaSonde high-frequency (HF) surface current mappers and wind forecasts were provided at 12 km resolution by the North American Mesoscale (NAM) model. First, the response of the surface currents to wind-forcing measured by five coastal National Data Buoy Center (NDBC) stations was evaluated using empirical orthogonal function (EOF) analysis. A significant correlation of approximately 0.8 was found between the majority of the variability in the seasonal anomalies of the low-pass filtered surface currents and the seasonal anomalies of the low-pass filtered wind stress measurements. The U and the V components of the measured surface currents were both shown to be forced by the zonal and meridional components of the wind-stress at the NDBC stations. Next, the NAM wind forecasts were tested for agreement with the measurements of the wind at the NDBC stations. Significant correlations of around 0.8 for meridional wind stress and 0.6 for zonal wind stress were found between the seasonal anomalies of the low-pass filtered wind stress measured by the NDBC stations and the seasonal anomalies of the low-pass filtered wind stress forecast by the NAM model. Given the amount of the variance in the winds captured by the NAM model and the response of the ocean surface currents to both components of the wind, bilinear regressions were formed relating the seasonal anomalies of the low-pass filtered NAM forecasts to the seasonal anomalies of the low-pass filtered surface currents. The regressions turned NAM wind forecasts into predictions of the seasonal anomalies of the low-pass filtered surface currents. Calculations of the seasonal cycle in the surface currents, added to these predicted seasonal anomalies, produced a non-tidal estimation of the surface currents that allowed a residual difference to be calculated from recent surface current measurements. The sum of the seasonal anomalies, the seasonal cycle, and the residual formed a prediction of the non-tidal surface currents. The average error in this prediction of the surface currents off the Oregon coast remained less than 4 cm/s out through 48 hours into the future.