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Item Bayesian hierarchical latent variable models for ecological data types(Montana State University - Bozeman, College of Letters & Science, 2022) Stratton, Christian Alexander; Chairperson, Graduate Committee: Jennifer Green and Andrew Hoegh (co-chair); This is a manuscript style paper that includes co-authored chapters.Ecologists and environmental scientists employ increasingly complicated sampling designs to address research questions that can help explain the impacts of climate change, disease, and other emerging threats. To understand these impacts, statistical methodology must be developed to address the nuance of the sampling design and provide inferences about the quantities of interest; this methodology must also be accessible and easily implemented by scientists. Recently, hierarchical latent variable modeling has emerged as a comprehensive framework for modeling a variety of ecological data types. In this dissertation, we discuss hierarchical modeling of multi-scale occupancy data and multi-species abundance data. Within the multi-scale occupancy framework, we propose new methodology to improve computational performance of existing modeling approaches, resulting in a 98% decrease in computation time. This methodology is implemented in an R package developed to encourage community uptake of our method. Additionally, we propose a new modeling framework capable of simultaneous clustering and ordination of ecological abundance data that allows for estimation of the number of clusters present in the latent ordination space. This modeling framework is also extended to accommodate hierarchical sampling designs. The proposed modeling framework is applied to two data sets and code to fit our model is provided. The software and statistical methodology proposed in this dissertation illustrate the flexibility of hierarchical latent variable modeling to accommodate a variety of data types.Item Pharmaceutical biomarkers to inform public and environmental health law and policy(Montana State University - Bozeman, College of Agriculture, 2020) Margetts, Miranda Lee; Chairperson, Graduate Committee: Robert K. D. Peterson and Deborah Keil (co-chair); Aparna Keshaviah, Cindy Hu, Victoria Troeger, Jordan Sykes, Nicholas Bishop, Tammy Jones-Lepp, Marisa Henry and Deborah E. Keil were co-authors of the article, 'Using wastewater-based epidemiology with local indicators of opioid and illicit drug use to overcome data gaps' submitted to the journal 'Journal of the American Medical Association' which is contained within this dissertation.; Terri Mavencamp, Jordan Sykes, Tammy Jones-Lepp, Nicholas Bishop, Victoria Troeger, Robert K. D. Peterson and Deborah E. Keil were co-authors of the article, 'The environmental impact of substance use in Montana's waterways: investigation of prescription, illicit, and recreational drug metabolite concentrations into receiving waters' which is contained within this dissertation.; Trent McCallson and Deborah E. Keil were co-authors of the article, 'Wastewater testing to support new environmental health compliance obligations in the healthcare industry' which is contained within this dissertation.The increasing awareness of the prevalence of prescription and illicit drug metabolites in wastewater is affecting changes to public and environmental health laws and policies. Drug takeback laws have been enacted to limit environmental pollution from drugs flushed into sewers; however, these laws only apply to legally prescribed drugs. Wastewater-based epidemiology, which relies on the measurement of drug concentrations in untreated wastewater, is also emerging as a complementary drug-use data tool to estimate drug consumption patterns by a community in near real-time. We sampled both the untreated influent and treated effluent at two locations in Montana over three months from April to June, 2019, to ascertain the concentrations of certain prescription and illicit drugs of abuse. The concentrations of drugs obtained from the untreated influent were used to inform a wastewater-based epidemiology study that compared drug-dose estimates from our wastewater samples against existing local drug-use sources (emergency medical services calls, drug seizures, and prescription dispense data). We also measured the treated effluent to determine the concentration at which drugs of abuse are persisting through the wastewater-treatment process and potentially affecting aquatic life exposed to those concentrations in receiving waters. We undertook a risk assessment whereby measured drug concentrations were assessed against corresponding ecotoxicology thresholds. Our results indicate that both codeine and morphine concentrations were above predicted no-effect concentrations. The overall results indicate that (1) wastewater-based epidemiology may be an effective tool to better describe substance abuse in communities and (2) drugs are persisting at levels above ecotoxicological thresholds from wastewater treatment plants into receiving waters. To our knowledge, these investigations are the first of their kind to have been conducted in Montana.Item Water quality response to water and nitrogen movement through a semi-arid dryland agroecosystem in Montana, USA(Montana State University - Bozeman, College of Agriculture, 2020) Sigler, William Adam; Chairperson, Graduate Committee: Stephanie A. Ewing; Stephanie A. Ewing, Clain A. Jones, Robert A. Payn, E.N. Jack Brookshire, Jane K. Klassen, Douglas Jackson-Smith and Gary S. Weissmann were co-authors of the article, 'Connections among soil, ground, and surface water chemistries characterize nitrogen loss from an agricultural landscape in the upper Missouri River Basin' in the journal 'Journal of hydrology' which is contained within this dissertation.; Stephanie A. Ewing, Clain A. Jones, Robert A. Payn, Perry Miller and Marco Maneta were co-authors of the article, 'Water and nitrate loss from dryland agricultural soils is controlled by management, soils, and weather' submitted to the journal 'Agricultural ecosystems & environment' which is contained within this dissertation.; Stephanie A. Ewing, Scott D. Wankel, Clain A. Jones, Sam Leuthold, E.N. Jack Brookshire and Robert A. Payn were co-authors of the article, 'Drivers of denitrification across a semiarid agroecosystem revealed by nitrate isotopic patterns' which is contained within this dissertation.Humans have increased reactive nitrogen (N) on the planet by an order of magnitude over the past 150 years. Most of this reactive N is used for fertilizer to feed a growing population, but loss of N from cultivated soils threatens agricultural and environmental sustainability. Nitrate accumulated in soil from fertilization or decomposition of soil organic N (SON) may be lost via leaching, which can reduce soil fertility and compromise water quality. Nitrate concentrations commonly exceed human drinking standards in groundwater resources around the globe. In the Judith River Watershed (JRW) in central Montana, nitrate has been detected above the standard since the 1960s. This dissertation contributes to a more holistic understanding of the fate and transport of N in the JRW. An interdisciplinary team engaged with farmers in a participatory research project, making observations in soils, groundwater, and streams to characterize water and N movement. At the landform scale, 5 to 9 cm yr -1 of the 38 cm yr -1 mean annual precipitation moves through soil to recharge groundwater and leaches 11 to 18 kg ha -1 yr -1 of nitrate-N from soil. These leaching rates are approximately 20-30% of fertilizer rates but likely reflect inmixing of nitrate from SON decomposition. Soil modeling analyses suggested that water and N losses were dominated by intense precipitation periods on wetter soils, such that more than half of simulated deep percolation and leaching occurred in two of 14 model years. Simulations further suggest that thinner soils (<25 cm fine-textured materials) experience water and nitrate loss rates five to 16 times higher than thicker soils (>100 cm). Soil sampling demonstrated that increased soil water during fallow periods facilitates conversion of SON to nitrate. Soils are then primed for water and N loss with subsequent precipitation, resulting in disproportionately high leaching rates during and following fallow periods. Isotopic evidence from fallow periods further suggests that nitrate is lost to the atmosphere via denitrification, a gas phase loss combining with leaching losses to compromise the goal of delivering N to crops. These findings suggest that reduction of fallow increases N use efficiency and reduces nitrate loss to groundwater.Item Towards a more-than-human geography of the Yellowstone River(Montana State University - Bozeman, College of Letters & Science, 2020) Bergmann, Nicolas Timothy; Chairperson, Graduate Committee: Jamie McEvoy; Jamie McEvoy, Elizabeth A. Shanahan, Eric D. Raile, Anne Marie Reinhold, Geoffrey C. Poole and Clemente Izurieta were co-authors of the article, 'Thinking through levees: how political agency extends beyond the human mind' in the journal 'Annals of the American Association of Geographers' which is contained within this thesis.This dissertation conceptualizes the Yellowstone River, flowing more than 670 miles from its headwaters in the mountains of northwestern Wyoming to its confluence with the Missouri River in western North Dakota, as a more-than-human assemblage. Specifically, this dissertation asks the following overarching research question: How does a more-than-human approach to understanding the Yellowstone River further geographical conceptualizations of human-environment relationships? In order to answer this question, this dissertation investigates the more-than-human aspects of both historical and contemporary environmental conflicts within Montana's portion of the Yellowstone River Basin. Chapter 2 examines the relationship between instream flow water law, Montana Fish and Game, and the Yellowstone River Basin. Drawing from both critical legal geography and political ecology, it furthers understandings of instream flow water law as relationally co-constituted through both human and nonhuman forces. Chapter 2 also traces the influence of Montana Fish and Game's more-than-anthropocentric ethical position on interpretations of the 1973 Montana Water Use Act. Chapter 3 uses a morethan- human approach to examine the relationship between myth and the Yellowstone River. Specifically, this chapter combines existing geographical understandings of myth with theories of assemblage and affect in order to historicize and denaturalize mythic belief in the Yellowstone as the longest undammed or free-flowing river remaining in the United States. Chapter 4 advances more-than-human understandings of political agency through a reframing of human thought as a co-constitutional assemblage of human and nonhuman elements. Relying on a comparative case study approach and qualitative interview data from two Montana communities located along the lower Yellowstone River, this chapter supports its theoretical claims through an embodied and affective analysis of the communities' divergent flood risk perceptions. Chapter 5 closes this dissertation with reflections on the value of using a more-than-human geographical approach.Item Understanding the present and past climate-fire-vegetation dynamics of southern South America (40 - 45°S)(Montana State University - Bozeman, College of Letters & Science, 2020) Ogunkoya, Ayodele Gilbert; Chairperson, Graduate Committee: Benjamin Poulter; David Roberts (co-chair); Jed O. Kaplan, Cathy Whitlock, William Nanavati, Benjamin Poulter and David Roberts were co-authors of the article, 'Drivers of modeled forest cover change in southern South America are linked to climate and CO^2' which is contained within this thesis.; Jed O. Kaplan, Cathy Whitlock, William Nanavati, Benjamin Poulter, David Roberts and Steve Hostetler were co-authors of the article, 'Climate drivers of late-glacial to postgalacial forest cover along the eastern Andes of Northern Patagonia (lat. 40 - 45°S)' which is contained within this thesis.The forest-steppe boundary that runs north-to-south along the eastern Andes is particularly dynamic over millennial time scales. Yet the relative role of long-term climate change and fire is poorly understood. In this study, I analyze the potential in using a process-based model in predicting species distribution, and the role fire and climate played in shaping the vegetation and treeline dynamics of Northern Patagonia (lat. 40 - 45 ° S). Paleoecological data, e.g., pollen, has been extensively used to study the relationship between climate and vegetation but has a low spatial resolution to distinguished between climate-fire-vegetation dynamics. Process-based model thus offers a transparent and robust method of incorporating a varying degree of complexity to understand fire behavior and fire-vegetation dynamics. Recently, LPJ-GUESS was parameterized to simulate major regional plant functional type (PFTs) and tree species distributions in this region. The model is able to predict regional species distribution across spatial scales by coupling establishment, growth, and mortality processes. Predicting spatial and temporal scale species distribution cannot be achieved without having the right climate and soil data, the climate data used was downscaled from 50 km to 1 km resolution using Worldclim climate data ( ~ 1 km) as the reference data. LPJ-GUESS model produced regional species distribution with fair to very good agreement with observation. The optimization of bioclimatic parameters and drought tolerance that is related to root depth, adaptability of plant to seasonal drought, and movement of nutrients consistently improved the accuracy of regional prediction of the species range. The model predicted that the vegetation distribution of present-day is mainly determined by climate and CO 2 rather than fire., while forest productivity responds strongly to elevated CO 2. However, based on the employed statistical methods of Canonical Correspondence Analysis (CCA) and Random Forest machine learning, combined with simulation results using paleoclimate. Results show that an increase in winter temperature drives the postglacial species distribution while changes in precipitation control radial growth and seedling establishment in the upper and lower treeline. These findings emphasize the importance of combining paleoecological methods with modeling to disentangle coarse-scale climate drivers from local influences.Item Green museums waking up the world: indigenous and mainstream approaches to exploring sustainability(Montana State University - Bozeman, College of Letters & Science, 2018) Medicine Horse, Jennifer Neso'eoo'e; Chairperson, Graduate Committee: Robert RydellMainstream and Indigenous Museums are ideally situated, both geographically and culturally, to educate the public about complex twenty-first century environmental issues. The most effective approaches to understanding, addressing, and adapting to these climate changes can be conveyed by museums, incorporating a holistic methodology utilizing the knowledge, observations and ideas of both Western and Indigenous peoples, and directed toward the young people of the world most impacted by climate disruption. This qualitative research was conceptualized iteratively within an Indigenous research methodology, using a combination of Western and Indigenous research approaches to create a hybrid methodology that would satisfy academic requirements, yet foster the community required to successfully answer the research question. Although a formal list of interview questions was developed, the qualitative interviews were primarily conducted in an informal conversational manner, allowing the respondents to tell their stories and include what they felt was relevant. A snowball strategy was employed to generate the potential interviews, as well as scouting potential interviews at the American Alliance of Museums (AAM) and Association of Tribal Archives Libraries and Museums (ATALM) annual conferences during the years 2011-2015. One hundred and three interviews were conducted at ten institutions; all interviews were conducted in-person on-site at the home institutions. Approximately half of the interviews were conducted at the Smithsonian Institution as the result of a Smithsonian Research Fellowship. The interview respondents were forthcoming about their experiences and observations regarding sustainability initiatives at their institutions. The interviews suggest that it is indeed possible for museums to address issues of climate disruption and sustainability efficaciously, utilizing both Western and Indigenous scientific knowledges to educate and engage the public. However, few American museums are currently attempting this task fraught with challenges, although museums are uniquely able to undertake this crucial work. The collaborative work catalyzed by the Cosmic Serpent and Native Universe NSF-funded research projects serves as a tested model to inspire museums to design their own initiatives. Citizen Science initiatives, engaging museums with their constituent youth, provide a promising way of conveying complex environmental information in a palatable manner to youth of various ages and cultural backgrounds.Item Motivation and pedagogical ecology of school-based outdoor science teaching: a multiple case study(Montana State University - Bozeman, College of Education, Health & Human Development, 2019) Vallor, Rosanna Rohrs; Chairperson, Graduate Committee: Ann EwbankThis study examines why and how teachers incorporate school-based outdoor teaching in their pedagogies. Research demonstrates that students gain in a range of areas when learning outdoors, but teachers can face multiple barriers when considering outdoor teaching, and many choose not to teach outdoors. There is limited research about why and how successful teachers choose to plan and manage outdoor teaching. Using a multiple case study of three public-school teachers, in grades 4, 7, and high school, who have consistently taught outdoors for over 15 years each, the study addressed why exemplary teachers choose to teach outdoors and how exemplary teachers accomplish outdoor teaching. Each teacher constituted an individual case. Semi-structured interview responses, questionnaires, field observation notes, and video-recall interviews were coded and analyzed using NVivo software. Analytic narratives based on themes within the coded data were then developed for individual cases, followed by cross-case analysis of the three cases. The findings indicated that the teachers were motivated to teach outdoors by perceived positive student impacts, by outstanding available outdoor spaces, and by their personal connections to the natural world. Teachers plan and manage outdoor teaching, with administration and community cooperation, to take advantage of opportunities for students to engage in their local environment. These findings were synthesized into the Pedagogical Ecology of Outdoor Teaching (PEOT) model. The PEOT model includes teachers' motivations, contextual factors, and teacher-operational factors in sequential, iterative relationship, and illustrates the complexity and uniqueness of teachers' situations when considering outdoor teaching. Future research incorporating the PEOT model could analyze teachers' contexts and environmental connections to determine assets and needs in their situations. Action plans to address those needs could then be developed to assist teachers and districts to develop outdoor teaching opportunities.Item Diethyl zinc mediated intramolecular metalloamination of N,N-dimethylhydrazines: expanding a novel approach to functionalized pyrrolidines and piperidines. Utilizing synthesis as a tool for medicinal chemistry, environmental remediation, and nonlinear optical chromophore construction(Montana State University - Bozeman, College of Letters & Science, 2017) Mickelsen, Ky James; Chairperson, Graduate Committee: Thomas S. Livinghouse; Dissertation contains an article of which Ky James Mickelsen is not the main author.; Sean Zabawa and Tom Livinghouse were co-authors of the article, 'Diethylzinc mediated metalloamination-alkylation of N,N-dimethylhydrazinoalkenes. Catalysis of carbon-zinc alkylation using simple copper(I) salts' in the journal 'Synlett' which is contained within this thesis.When attempting to develop a novel material for increased second-order nonlinear activity, a strategy was devised to rationally design an architecture that would allow for optimized acentric supramolecular organization. By coupling a liquid crystal tolane to a well-understood NLO chromophore via strategic synthesis, a set of novel chromophores was created. The ferroelectric liquid crystal-like molecules intrinsically favor unidirectional chromophore order while simultaneously containing a high beta chromophore along the polar axis. This system has shown potential for high terminal stability as well as increased nonlinear optical susceptibilities. Carbon tetrachloride poses a large threat to the environment and is the focus of ongoing remediation efforts. It is a well-known carcinogenic pollutant that has contaminated groundwater beneath former grain storage and industrial sites, such as the Department of Energy's Hanford site. Remediation through the use of a small molecule, PDTC, when complexed with copper has been shown to lead to complete dechlorination, resulting in conversion to non-toxic end-products (mostly CO 2) and complete removal of the problematic carbon-chlorine bonds. Synthetic chemistry was employed to develop a modified procedure for large-scale production of PDTC that eliminates harmful byproducts and excess toxic reagents used. Additionally, structural derivatives for increased water solubility have been envisaged from citrazinic acid, which could allow for aqueous destruction of carbon tetrachloride. In medicinal and pharmaceutical chemistry, routes to nitrogenous heterocycles are of great importance due to their prevalence in bioactive molecules. Diethylzinc mediated metalloamination/cyclization of unsaturated N,N-dimethylhydrazines with subsequent electrophilic functionalization could prove to be a powerful tool for constructing pyrrolidines and piperidines. This method was extended to the use of 1,2-disubstituted alkenes as N-Zn migratory insertion acceptors, including various vinylcyclopropyl hydrazines. The potential behind the irreversible cyclopropane scission and development of a new alkene make this class of substrates extremely desirable. The metalloamination-alkylation of N,N-dimethylhydrazinoalkenes was shown to be effectively catalyzed by CuBr x SMe 2, CuCN and CuI. This novel method obviates the prior methodology involving use of stoichiometric CuCN(LiCl) 2 as a promoter for the electrophilic functionalization.Item A spatiotemporal analysis of climate change in the Greater Yellowstone Ecosystem and its effects on Pinus albicaulis(Montana State University - Bozeman, College of Letters & Science, 2017) Chang, Tony; Chairperson, Graduate Committee: Andrew J. Hansen; Andrew J. Hansen was a co-author of the article, 'Historic and projected climate change in the Greater Yellowstone Ecosystem' in the journal 'Yellowstone science' which is contained within this thesis.; Andrew J. Hansen and Nathan Piekielek were co-authors of the article, 'Patterns and variability of projected bioclimatic habitat for Pinus albicaulis in the Greater Yellowstone area' in the journal 'PLoS one' which is contained within this thesis.; Andrew J. Hansen, Jesse Logan, Mark C. Greenwood, David W. Roberts and Jia Hu were co-authors of the article, 'A comparative severity analysis of recent Dendroctonus ponderosae outbreak and predictive hindcasts within the Greater Yellowstone Ecosystem' which is contained within this thesis.Climate change is arguably the biggest challenge facing humanity. Successful mitigation and adaption planning vitally requires more science in regard to its impacts on ecological systems. To address knowledge gaps regarding climate change impacts within the regional level, I performed a series of analyses on an "early responder" species in the Greater Yellowstone Ecosystem and examine how its distribution may be impacted by biotic and abiotic factors. My research aids in decision making processes for regional land managers that must address climate change in their policy decisions and increases ecological understanding at a landscape level. This manuscript includes a detailed analysis of past, present, and projected climate in the Greater Yellowstone Ecosystem. I addressed the expected impacts of present and future climate shifts on the distribution of the sub-alpine tree species, whitebark pine (Pinus albicaulis) and its main disturbance agent, mountain pine beetle (Dendroctonus ponderosae). This research found a major reduction of suitable climate habitat for P.albicaulis within the Greater Yellowstone Ecosystem under multiple Global Circulation Models and Representative Concentration Pathway futures. Finally, this research determined that the recent D.ponderosae outbreak driven by climate effects in 2000-2010, that resulted in an unprecedented mortality event on P.albicaulis was more than double the risk area size of any previous outbreak since 1951. Although more studies are necessary to reduce uncertainty and make assertive recommendations for management actions, this research suggests that future sub-alpine stand structure and composition may be radically different than anything in recent history due to range shifts of suitable climate habitat and disturbance agents, and advocates for land managers to apply a multifaceted approach of competitor thinning and controlled burning to ensure the resilience and persistence of P.albicaulis.Item Factors influecing the abundance of microorganisms in icy environments(Montana State University - Bozeman, College of Agriculture, 2016) Santibanez-Avila, Pamela Alejandra; Chairperson, Graduate Committee: John C. Priscu; Joseph R. McConnell and John C. Priscu were co-authors of the article, 'A flow cytometric method to measure prokaryotic records in ice cores: an example from the Wais Divide drilling site' submitted to the journal 'Journal of glaciology: instruments and methods' which is contained within this dissertation.; Mark Greenwood, Joseph R. McConnell and John C. Priscu were co-authors of the article, 'Prokaryotic concentration changes between the last glacial maximum and the early Holocene from the Wais Divide ice core' submitted to the journal 'Quaternary science reviews' which is contained within this dissertation.; Alexander B. Michaud, Trista J. Vick-Majors, Juliana D'Andrilli, Amy Chiuchiolo and John Priscu were co-authors of the article, 'Bacterial response to progressive freezing in perennially and seasonally ice-covered lakes' submitted to the journal 'Journal of geophysical research (JGR) biogeosciences' which is contained within this dissertation.Microbial life can easily live without us; we, however, cannot survive without the global catalysis and environmental transformations it provides' (Falkowski et al., 2008). Despite of the key role of microbes on Earth, microbial community characteristics are not explicitly part of climate models because our understanding of their responses to long-term environmental and climatic processes is limited. In this study, I developed a Flow Cytometric protocol to access a long-term record of non-photosynthetic prokaryotic cell concentration archived in the West Antarctic Ice-Sheet (WAIS; chapter 2). The WD ice core was retrieved between 2009 and 2011 to a depth of 3,405 m, extending back to 68,000 before 1950. Once a 17,400 year-record of prokaryotic cell concentration was acquired, I investigated its temporal variability and patterns, determined the potential sources of prokaryotic cells between the Last Glacial Maximum and the early Holocene, and assessed the environmental factors that might have the largest influence on the prokaryotic response (chapter 3). The observed patterns in the prokaryotic record are linked to large-scale controls of the Southern Ocean and West Antarctica Ice-Sheet. The main research findings presented here about the first prokaryotic record are: (i) airborne prokaryotic cell concentration does respond to long-term climatic and environmental processes, (ii) the processes of deglaciation, sea level rise and sea-ice fluctuation were key; the abundance of prokaryotic cells covariate with ssNa and black carbon, and (iii) the prokaryotic cell record variate on millennial time scale with cycles of 1,490-years. In addition, I studied 'congelation ice' (i.e., ice forms as liquid water freezes) from ice-covered lakes to understand prokaryotic cell segregation between liquid and solid phases during the physical freezing process. Five mesocosm experiments were designed to understand prokaryotic responses to the progressive freezing in concert with field observations from ice-covered lakes from Barrow, Alaska. As a result of this last study (chapter 4), I concluded that prokaryotic cells are preferentially incorporated in the ice with segregation coefficients (K eff) between 0.8 - 4.4, which are higher than for major ions. Prokaryotic cells avoid rejection more effectively from the ice matrix.