<p><italic>Cryptococcus gattii</italic> has been actively emerging and adapting to the climates and environment in western North America, bringing with it life-threatening disease to humans and animals. Through systematic investigations of the dynamics of this pathogen in the United States, by studying outbreaks and individual cases, our studies have aimed to increase the understanding of the expansion, emergence, pathogenicity, molecular epidemiology, population structure, and speciation dynamics of this organism that had previously been largely restricted to tropical and sub-tropical climates of the world. <BR> <BR></p><p>Molecular sequence typing has revealed that there are four distinct <italic>C. gattii</italic> molecular types (VGI-VGIV). A major focus of our efforts to examine this pathogen in the United States surrounds the unprecedented <italic>C. gattii</italic> outbreak that emerged in British Columbia, Canada in 1999 and has since expanded throughout the Pacific Northwest region of the United States (Chapters 2, 3). This outbreak has resulted in a large number of infections in both humans and animals, including a high percentage of otherwise healthy individuals. The outbreak isolates are primarily molecular type VGIIa (the major genotype), VGIIb (the minor genotype), or VGIIc, a novel genotype that emerged in Oregon in approximately 2005. <BR> <BR></p><p>The North American Pacific Northwest harbors one of the highest incidences of <italic>C. gattii</italic> infections. In an expansion of molecular epidemiology and population analysis of both MLST and VNTR markers, we show that the VGIIc group is clonal and hypothesize it arose recently. The VGIIa/c outbreak lineages are sexually fertile and studies support ongoing recombination in the global VGII population. This illustrates two hallmarks of emerging outbreaks: high clonality and the emergence of novel genotypes via recombination. In macrophage and murine infections, the novel VGIIc genotype and VGIIa/major isolates from the United States are highly virulent compared to similar non-outbreak VGIIa/major-related isolates. Molecular analysis distinguishes clonal expansion of the VGIIa/major outbreak genotype from related but distinguishable less-virulent genotypes isolated from other geographic regions. Our evidence documents emerging hypervirulent genotypes in the United States that may expand further and provides insight into the possible molecular and geographic origins of the outbreak. <BR> <BR></p><p>While the outbreak is a significant public health concern, an overlooked but considerable disease burden attributable to <italic>C. gattii</italic> among HIV/AIDS patients in Southern California has also occurred (chapter 4). In our studies, we examined the molecular epidemiology, population structure, and virulence attributes of <italic>C. gattii</italic> isolates collected from a cohort of HIV/AIDS patients in Los Angeles County, California. We show that these isolates consist almost exclusively of VGIII molecular type (>93%), in contrast to the vast majority of VGII molecular type isolates found in the outbreak region. Based on molecular phylogenetic analysis, the global VGIII population structure can be divided into two groups, VGIIIa and VGIIIb. We show that isolates from the Californian patients are virulent in murine and macrophage models of infection, with VGIIIa significantly more virulent than VGIIIb. Several VGIII isolates are highly fertile and able to produce large numbers of spores that may serve as infectious propagules. Based on molecular analysis, the a and &alpha; VGIII MAT locus alleles are largely syntenic with limited rearrangements compared to the known VGI (a/&alpha;) and VGII (&alpha;) <italic>MAT</italic> loci, but each has unique characteristics including a distinct deletion flanking the 5' VGIII <italic>MAT</italic> <bold>a</bold> alleles. Fingerprinting analyses of the MAT locus shows that the &#945; allele is more heterogeneous than the <bold>a</bold>allele. Our studies indicate that <italic>C. gattii</italic> VGIII is endemic in Southern California, with other isolates originating from the neighboring regions of Mexico, and in some rarer cases from Oregon and Washington state. Given that >1,000,000 cases of cryptococcal infection and >620,000 attributable mortalities occur annually in the context of the global AIDS pandemic, our findings suggest a significant burden of <italic>C. gattii</italic> infection in AIDS patients may be unrecognized, with potential prognostic and therapeutic implications. These results signify the need to classify pathogenic Cryptococcus cases and highlight possible host differences among the <italic>C. gattii</italic> molecular types, influencing infection of immunocompetent (VGI/VGII) vs. immunocompromised (VGIII/VGIV) hosts. <BR> <BR></p><p>In 2007, the first confirmed case of <italic>Cryptococcus gattii</italic> was reported in the state of North Carolina, USA (chapter 5). An otherwise healthy HIV- male patient presented with a large upper thigh cryptococcoma in February, which was surgically removed and the patient was started on long-term high-dose fluconazole treatment. In May of 2007, the patient presented to the emergency room with seizures. Magnetic resonance imaging revealed two large CNS lesions found to be cryptococcomas based on brain biopsy. Prior chest CT imaging had revealed small lung nodules indicating that <italic>C. gattii</italic> spores or desiccated yeast were likely inhaled into the lungs and dissemination occurred to both the leg and CNS. The patient's travel history included a visit throughout the San Francisco, California region in September-October of 2006, consistent with acquisition during this time period. Cultures from both the leg and brain biopsies were subjected to analysis. Both isolates were <italic>C. gattii</italic>, VGI molecular type. Based on molecular studies and virulence in a heterologous host model, the leg and brain isolates are identical, but the two differed in mating fertility. Two clinical isolates, one from a transplant recipient in San Francisco and the other from Australia, were identical to the North Carolina isolate at all markers tested. Closely related isolates that differ at only one or a few noncoding markers are present in the Australian environment. Our findings support a model in which <italic>C. gattii</italic> VGI was transferred from Australia to California, possibly though an association with its common host plant <italic>E. camaldulensis</italic>, and the patient was exposed in San Francisco and returned to present with disease in North Carolina. <BR> <BR></p><p>To elucidate the speciation dynamics between molecular types VGII and VGIII and what influence nuclear and mitochondrial genomes have on intracellular proliferation and hyoervirulence, we conducted a comprehensive analysis of progeny sets between these molecular types, including progeny sets of VGII<bold>a</bold> x VGIII&alpha; and VGII&alpha; x VGIII<bold>a</bold> crosses (chapter 6). Our analysis reveals that spore viability is exceedingly low, supporting that these are distinct species. We also found that the mitochondrial genome of virulent strains may be necessary but not fully sufficient to confer virulence characteristics. These studies show that each molecular type is likely a distinct species, which was further supported by high levels of diploid or aneuploid progeny, and also shed light into the possible control that both the mitochondrial and nuclear genomes may play in hypervirulence of <italic>C. gattii</italic> outbreak genotypes. Future analyses of both the regions regulating the virulence and also the generation of progeny sets between other species will further address the roles of both speciation and virulence evolution in <italic>C. gattii</italic>. <BR> <BR></p><p>Overall, the studies documented in this dissertation have increased the understanding of molecular epidemiology, population structures, fertility, phenotypic characteristics, virulence characterizations, and speciation of this expanding and emerging fungal pathogen in the United States. This dissertation adds a foundation to the studies of <italic>C. gattii</italic> in the United States and enables future research to be conducted in several critical areas to better understand and ultimately influence surveillance, prognosis, and treatment of patients and animals in future years.</p> / Dissertation

The American pika (Ochotona princeps) finds moderately warm temperatures (>25°C) lethally stressful, and at the end of the last Ice Age 10,000 years ago was forced to disperse to cooler, "sky island" mountaintops where they are almost exclusively found today. Thirty six subspecies are recognized, all established using morphological characters, and it is uncertain whether these subspecies' designations are corroborated by genetic analyses. This study elucidates three hypotheses regarding populations in Oregon and southern Washington: 1) O. p. fumosa constitutes a subspecies distinct form O. p. brunnescens, 2) the Columbia River constitutes a barrier to gene flow giving rise to two subspecies rather than the single subspecies O. p. brunnescens, and 3) populations in eastern Oregon ( O. p. jewetti and O. p. taylori) are genetically distinct from populations in the Cascade Range ( 0. p. brunnescens and O. p. fumosa).

Focusing on the relationship between demography and sedentary behavior, this thesis explores changes to mobility strategies on the Northern Northwest Coast of North America between 11,000 and 5,000 cal BP. Drawing on a regional database of radiocarbon dates, it uses summed probability distributions (SPDs) of calibrated dates as a proxy for population change, in combination with syntheses of previously published technological, paleo environmental and settlement pattern data to test three hypotheses derived from the literature about the development of logistic mobility among maritime hunter-gatherers on the Northern Coast. In all, each of the hypotheses proposes that early peoples on the coast were foragers that utilized high levels of residential mobility, who later adopted collector (logistic) strategies. Two of the hypotheses emphasize the role of population growth and/or packing and resource distribution in this transformation, while the third emphasizes population replacement. Other issues addressed within this thesis are whether or not the forager-collector continuum, as it is used for terrestrial hunter-gatherers, can be applied to those in aquatic settings. Also explored, is the question of whether the available data is sufficient for making and/or testing claims about early mobility patterns in the region. The results of the demographic models suggest that while population levels were volatile, volatility declined through time and that there is no significant trend in either growth or decline of overall population levels throughout the region. This thesis also confirmed that significant changes to mobility, as evidenced by the emergence of semi-sedentary to sedentary living, begin to appear by ~7,000 cal BP. However, there appears to be little, if any correlation between the advent of more sedentary and logistic behavior and any of the variables tested here. Thus this author suggests, in agreement with Ames (1985; 2004) and Binford (2001) that the distribution of resources and labor organization needs within aquatic environments are sufficient without any other drivers for the development and intensification of logistic mobility. The principle analytic contribution of this research comes from the demographic modeling that relied on the construction of summed probability distributions. Though these methods have become commonplace in other settings (namely Europe), this thesis presents the first application of these methods within the time period and region covered. Moreover, this research is one of the only of its kind to address demographic histories within coastal landscapes that utilizes both marine and terrestrial 14C samples. In order to explore possible biases within the database, comparisons of marine and terrestrial SPDs were made between sub-sections of the region (i.e. Haida Gwaii, Southeast Alaska and the Dundas Islands). Though patterning between each of these areas was consistent, these comparative methods revealed an unexpected finding; a massive population crash throughout the region that began between ~9,000-8,800 cal BP and lasted till around 8,400 cal BP. Importantly, this crash was witnessed within all of the individual sub-areas and within SPDs made from both the marine and terrestrial 14C samples, though the reasons behind this collapse and verification of its existence require future research. However, finding this collapse at all further highlighted the need for use of correctly calibrated 14C dates, as the gap in 14C dates effectively disappears when using uncalibrated dates, which has been a longstanding tradition within Northwest archaeology.

Incremental growth rings in X-rays of salmon vertebrae have been used since the 1980s to age Pacific salmon (Oncorhynchus spp.) remains from archaeological sites in the Pacific Northwest. These age estimates, paired with generalized life history patterns, have been used to determine salmon species, season of capture and in turn season of site occupation. This approach relies on a variety of assumptions, the most fundamental of which is that rings represent true years. Archaeologists using vertebral age determination techniques have failed to adequately test this assumption and present their methodologies. This thesis assesses the validity of using incremental growth structures in Chinook salmon (Oncorhynchus tshawytscha) vertebrae to determine the age at death of fish represented in archaeological sites. This project develops criteria and a protocol for the identification of true annuli and tests these identifications on a collection of modern Chinook salmon of known age. Finally, this protocol is applied to archaeological remains of Chinook from Cathlapotle (45CL1). Three collections of modern known age fish (N=121) were used to evaluate and test approaches to aging Chinook salmon with vertebrae. These collections contained juvenile and adult Chinook from throughout Washington and Oregon. I evaluated a variety of methods for viewing rings including magnified surface images, X-ray images and thin sections to determine which is the most accurate, reliable and efficient, also considering the extent of specimen destruction. Rings visible in X-rays were found to reflect the internal structure of vertebrae rather than annular growth. The number of these internal walls did not correspond to the known ages of fish and are therefore not true annuli. Criteria previously described by salmon fisheries biologist were used to isolate annuli (on the centrum surface) on the Hanford reach collection (N=46). In a test for accuracy 39 (85%) were aged correctly. In a test of reliability utilizing five additional readers all but 14 cases showed discrepancies among readers. Results of the test of reliability were not as successful as other researchers in fisheries biology but given the high accuracy rate the method remains valid. The final goal of this project was to determine the feasibility of applying the surface ring method of age determination to archaeological collections. Archaeological salmon vertebrae from Cathlapotle (45CL1) on the lower Columbia River, Washington state were utilized. One hundred salmon vertebrae were selected and classified to species according to Huber et al. (2011); 89 were identified as Chinook. Of these, 39 had sufficient preservation of the surface to view and interpret incremental rings. Three ages were identified 3, 4 and 5 year olds. This ageing protocol can be applied to archaeological Chinook salmon vertebrae to estimate age of ancient Chinook salmon. Additional work is needed on other salmon species to demonstrate the methods validity across all salmonid species. This analysis has great potential for modeling salmon paleo-life history by contributing data from salmon populations prior to the major impacts of the 19th and 20th century. This is particularly valuable for salmon conservation because information on size, the timing and duration of freshwater emigration as well as the age of spawning and death is critical to the management of hatchery and wild salmon populations.

Speciation is the process by which life diversifies into discrete forms, and understanding its underlying mechanisms remains a primary focus for biologists. Increasingly, empirical studies are helping explain the role of ecology in generating biodiversity. Adaptive radiations are often propelled by selective fitness tradeoffs experienced by individuals that invade new habitats, resulting in reproductive isolation from ancestral conspecifics and potentially cladogenesis. Host specialist insects are among the most speciose organisms known and serve as highly useful models for studying adaptive radiations. We are just beginning to understand the pace and degree with which these insects diversify. The apple maggot, Rhagoletis pomonella, is a well-studied insect whose eastern and southern populations are models for ecological speciation. Recently (40–65 ya), the fly has invaded the Pacific Northwestern United States through human-transported apples infested with larvae. There, populations of R. pomonella have rapidly colonized two novel hawthorn hosts whose fruiting times bracket apple’s (early-season native Crataegus douglasii and introduced C. monogyna, which fruits late in the season). The recent introduction might initiate host shifts, providing opportunities to examine the pace and mechanistic means with which host races (an evolutionary stage preceding speciation) become established. Here, I demonstrate that host-associated populations at a site in southwest Washington are partially allochronically isolated from one another, and life cycles temporally match with natal host fruit ripening times in sympatry. If spatially widespread, these temporal barriers could result in reproductive isolation and possibly cladogenesis. Implications of these findings reach beyond academic import, as R. pomonella is expanding not only its host range, but its geographic range is encroaching upon central Washington, the site of a multi-billion dollar per year apple-growing industry.

At the end of the 18th century, Anglo Americans and Europeans entered the mouth of the Columbia River for the first time. There they encountered large villages of Chinookan and other Native Americans. Soon afterwards, the Chinookan People became involved in the global fur trade. Pelts, supplies, and native made goods were exchanged with fur traders, who in return provided Chinookans with a number of trade goods. Over the next 40 years, life changed greatly for the Chinookans; new trade and political alliances were created, foreign goods were introduced, and diseases killed large portions of the population (Hajda 1984; Gibson 1992; Schwantes 1996; Boyd 2011; Boyd et al. 2013). Additionally, fur trade forts, like the Hudson's Bay Company's (HBC) Fort Vancouver, were established. At these forts, new multiethnic communities were created to support the fur trade economy (Hussey 1957; Kardas 1971; Warner and Munnik 1972; Erigero 1992; Burley 1997; Mackie 1997; Wilson 2010). This thesis is an historical archaeological study of how Chinookan peoples at three villages and employees of the later multicultural Village at Fort Vancouver negotiated the processes of contact and colonization. Placed in the theoretical framework of practice theory, everyday ordinary activities are studied to understand how cultural identities are created, reinforced, and changed (Lightfoot et al. 1998; Martindale 2009; Voss 2008). Additionally uneven power relationships are examined, in this case between the colonizer and the colonized, which could lead to subjugation but also resistance (Silliman 2001). In order to investigate these issues, this thesis studies how the new foreign material of vessel glass was and was not used during the everyday practice of tool production. Archaeological studies have found that vessel glass, which has physical properties similar to obsidian, was used to create a variety of tool forms by cultures worldwide (Conte and Romero 2008). Modified glass studies (Harrison 2003; Martindale and Jurakic 2006) have demonstrated that they can contribute important new insights into how cultures negotiated colonization. In this study, modified glass tools from three contact period Chinookan sites: Cathlapotle, Meier, and Middle Village, and the later multiethnic Employee Village of Fort Vancouver were examined. Glass tool and debitage analysis based on lithic macroscopic analytical techniques was used to determine manufacturing techniques, tool types, and functions. Additionally, these data were compared to previous analyses of lithics and trade goods at the study sites. This thesis demonstrates that Chinookans modified glass into tools, though there was variation in the degree to which glass was modified and the types of tools that were produced between sites. Some of these differences are probably related to availability, how glass was conceptualized by Native Peoples, or other unidentified causes. This study suggests that in some ways glass was just another raw material, similar to stone, that was used to create tools that mirrored the existing lithic technology. However at Cathlapotle at least, glass appears to have been relatively scarce and perhaps valued even as a status item. While at Middle Village, glass (as opposed to stone) was being used about a third of the time to produce tools. Glass tool technology at Cathlapotle, Meier, and Middle Village was very similar to the existing stone tool technology dominated by expedient/low energy tools; however, novel new bottle abraders do appear at Middle Village. This multifaceted response reflects how some traditional lifeways continued, while at the same time new materials and technology was recontextualized in ways that made sense to Chinookan peoples. Glass tools increase at the Fort Vancouver Employee Village rather than decrease through time. This response appears to be a type of resistance to the HBC's economic hegemony and rigid social structure. Though it is impossible to know if such resistance was consciously acted on or was just part of everyday activities that made sense in the economic climate of the time. Overall, this thesis demonstrates how a mundane object such as vessel glass, can provide a wealth of information about how groups like the Chinookans dealt with a changing world, and how the multiethnic community at Fort Vancouver dealt with the hegemony of the HBC. Chinookan peoples and the later inhabitants of the Fort Vancouver Employee Village responded to colonization in ways that made sense to their larger cultural system. These responses led to both continuity and change across time.

This thesis estimates the impacts of rooftop photovoltaic (PV) capacity on electricity generation and CO2 emissions in America's Pacific Northwest. The region's demand for electricity is increasing at the same time that it is attempting to reduce its greenhouse gas emissions. The electricity generated by rooftop PV capacity is expected to displace electricity from fossil fueled electricity generators and reduce CO2 emissions, but when and how much? And how can this region maximize and focus the impacts of additional rooftop PV capacity on CO2 emissions? To answer these questions, an hourly urban rooftop PV generation profile for 2009 was created from estimates of regional rooftop PV capacity and solar resource data. That profile was compared with the region's hourly fossil fuel generation profile for 2009 to determine how much urban rooftop PV generation reduced annual fossil fuel electricity generation and CO2 emissions. Those reductions were then projected for a range of additional multiples of rooftop PV capacity. The conclusions indicate that additional rooftop PV capacity in the region primarily displaces electricity from natural gas generators, and shows that the timing of rooftop PV generation corresponds with the use of fossil fuel generators. Each additional Wp/ capita of rooftop PV capacity reduces CO2 emissions by 9,600 to 7,300 tons/ year. The final discussion proposes some methods to maximize and focus rooftop PV impacts on CO2 emissions, and also suggests some questions for further research.

Stress is a fact of life. There has been much research done since the early 1970's dealing with the various aspects and relationships of stress and life events for all stages of human development. The purpose of this study was to investigate perceived life-event stressors of 9th grade and 12th grade students in three Pacific Northwest rural schools. The study also sought to a) ascertain whether male students in the 9th grade and 12th grade perceive stressful life events differently than female students in the same grade, and b) explore if there was a difference in perceptions of students of "different" rural community populations and different age populations (9th & 12th graders).

This study examines how regional cuisine is being self-consciously constructed in the Pacific Northwest and discusses the ways in which it contributes to identity in the region. I identify the characteristics-foods, dishes, and culinary practices-of this "new" Northwest cuisine, as well as social and cultural values associated with it, and explore how together they create a sense of regional distinctiveness and loyalty. Because this type of regional cuisine is closely associated with the professional cooking community, I look to restaurants in Portland, Oregon that self-identity as representative of the Pacific Northwest and to regional cookbooks, in order to pinpoint the characteristics of Northwest cuisine and explore their regional associations. I draw on a number of qualitative methods: an analysis of regional cookbooks, a restaurateur survey, interviews with restaurateurs, and a restaurant menu analysis. The use of the region's many specialty agricultural products-berries, orchard fruits, hazelnuts, and mushrooms-in meat, game, fish and seafood dishes, as well as salads, are defining aspects of Northwest cuisine. Salmon, more so than any other foodstuff, is the quintessential Northwest food. It is historically significant and has reached iconic status in the Pacific Northwest. Because of their association with the region's agricultural history and in some cases its cultural history, regional foodstuffs and the dishes they are used in help satisfy a growing hunger for regional identity and a sense of place among Northwesters. The past these foodstuffs are associated with is idealized and based on the same "Eden" metaphor that brought many settlers to the region during the mid-nineteenth century. By emphasizing the use of regional foodstuffs rather than a shared culinary history, Northwest cuisine embraces new residents from diverse backgrounds as well as "natives."

The following study is designed to look at one religious group and assess some of the social service needs as seen by the study participants. Since social services cover such a broad spectrum, it was decided to limit the study to marital counseling needs and related issues as seen by individual church members.