ASU Electronic Theses and Dissertations
This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
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- All Subjects: Biology
- Creators: Fenichel, Eli
Description
Consideration of both biological and human-use dynamics in coupled social-ecological systems is essential for the success of interventions such as marine reserves. As purely human institutions, marine reserves have no direct effects on ecological systems. Consequently, the success of a marine reserve depends on managers` ability to alter human behavior in the direction and magnitude that supports reserve objectives. Further, a marine reserve is just one component in a larger coupled social-ecological system. The social, economic, political, and biological landscape all determine the social acceptability of a reserve, conflicts that arise, how the reserve interacts with existing fisheries management, accuracy of reserve monitoring, and whether the reserve is ultimately able to meet conservation and fishery enhancement goals. Just as the social-ecological landscape is critical at all stages for marine reserve, from initial establishment to maintenance, the reserve in turn interacts with biological and human use dynamics beyond its borders. Those interactions can lead to the failure of a reserve to meet management goals, or compromise management goals outside the reserve. I use a bio-economic model of a fishery in a spatially patchy environment to demonstrate how the pre-reserve fisheries management strategy determines the pattern of fishing effort displacement once the reserve is established, and discuss the social, political, and biological consequences of different patterns for the reserve and the fishery. Using a stochastic bio-economic model, I demonstrate how biological and human use connectivity can confound the accurate detection of reserve effects by violating assumptions in the quasi-experimental framework. Finally, I examine data on recreational fishing site selection to investigate changes in response to the announcement of enforcement of a marine reserve in the Gulf of California, Mexico. I generate a scale of fines that would fully or partially protect the reserve, providing a data-driven way for managers to balance biological and socio-economic goals. I suggest that natural resource managers consider human use dynamics with the same frequency, rigor, and tools as they do biological stocks.
ContributorsFujitani, Marie (Author) / Abbott, Joshua (Thesis advisor) / Fenichel, Eli (Thesis advisor) / Gerber, Leah (Committee member) / Anderies, John (Committee member) / Arizona State University (Publisher)
Created2014
Description
Many studies over the past two decades examined the link between climate patterns and discharge, but few have attempted to study the effects of the El Niño Southern Oscillation (ENSO) on localized and watershed specific processes such as nutrient loading in the Southwestern United States. The Multivariate ENSO Index (MEI) is used to describe the state of the ENSO, with positive (negative) values referring to an El Niño condition (La Niña condition). This study examined the connection between the MEI and precipitation, discharge, and total nitrogen (TN) and total phosphorus (TP) concentrations in the Upper Salt River Watershed in Arizona. Unrestricted regression models (UMs) and restricted regression models (RMs) were used to investigate the relationship between the discharges in Tonto Creek and the Salt River as functions of the magnitude of the MEI, precipitation, and season (winter/summer). The results suggest that in addition to precipitation, the MEI/season relationship is an important factor for predicting discharge. Additionally, high discharge events were associated with high magnitude ENSO events, both El Niño and La Niña. An UM including discharge and season, and a RM (restricting the seasonal factor to zero), were applied to TN and TP concentrations in the Salt River. Discharge and seasonality were significant factors describing the variability in TN in the Salt River while discharge alone was the significant factor describing TP. TN and TP in Roosevelt Lake were evaluated as functions of both discharge and MEI. Some significant correlations were found but internal nutrient cycling as well as seasonal stratification of the water column of the lake likely masks the true relationships. Based on these results, the MEI is a useful predictor of discharge, as well as nutrient loading in the Salt River Watershed through the Salt River and Tonto Creek. A predictive model investigating the effect of ENSO on nutrient loading through discharge can illustrate the effects of large scale climate patterns on smaller systems.
ContributorsSversvold, Darren (Author) / Neuer, Susanne (Thesis advisor) / Elser, James (Committee member) / Fenichel, Eli (Committee member) / Arizona State University (Publisher)
Created2012
Description
The southwestern willow flycatcher (Empidonax traillii extimus) is listed as an endangered species throughout its range in the southwestern United States. Little is known about its sub-population spatial structure and how this impacts its population viability. In conjunction with being listed as endangered, a recovery plan was produced by the US Fish and Wildlife Service, with recovery units (sub-populations) roughly based on major river drainages. In the interest of examining this configuration of sub-populations and their impact on the measured population viability, I applied a multivariate auto-regressive state-space model to a spatially extensive time series of abundance data for the southwestern willow flycatcher over the period spanning 1995-2010 estimating critical growth parameters, correlation in environmental stochasticity or "synchronicity" between sub-populations (recovery units) and extinction risk of the sub-populations and the whole. The model estimates two parameters, the mean and variance of annual growth rate. Of the models I tested, I found the strongest support for a population model in which three of the recovery units were grouped (the Lower Colorado, Gila Basin, and Rio Grande recovery units) while keeping all others separate. This configuration has 6.6 times more support for the observed data than a configuration assigning each recovery unit to a separate sub-population, which is how they are circumscribed in the recovery plan. Given the best model, the mean growth rate is -0.0234 (CI95 -0.0939, 0.0412) with a variance of 0.0597 (CI95 0.0115, 0.1134). This growth rate is not significantly different from zero and this is reflected in the low potential for quasi-extinction. The cumulative probability of the population experiencing at least an 80% decline from current levels within 15 years for some sub-populations were much higher (range: 0.129-0.396 for an 80% decline). These results suggest that the rangewide population has a low risk of extinction in the next 15 years and that the formal recovery units specified by the original recovery plan do not correspond to proper sub-population units as defined by population synchrony.
ContributorsDockens, Patrick E. T. (Author) / Sabo, John (Thesis advisor) / Stromberg, Juliet (Committee member) / Fenichel, Eli (Committee member) / Arizona State University (Publisher)
Created2012
Description
The ability to tolerate bouts of oxygen deprivation varies tremendously across the animal kingdom. Adult humans from different regions show large variation in tolerance to hypoxia; additionally, it is widely known that neonatal mammals are much more tolerant to anoxia than their adult counterparts, including in humans. Drosophila melanogaster are very anoxia-tolerant relative to mammals, with adults able to survive 12 h of anoxia, and represent a well-suited model for studying anoxia tolerance. Drosophila live in rotting, fermenting media and a result are more likely to experience environmental hypoxia; therefore, they could be expected to be more tolerant of anoxia than adults. However, adults have the capacity to survive anoxic exposure times ~8 times longer than larvae. This dissertation focuses on understanding the mechanisms responsible for variation in survival from anoxic exposure in the genetic model organism, Drosophila melanogaster, focused in particular on effects of developmental stage (larval vs. adults) and within-population variation among individuals.
Vertebrate studies suggest that surviving anoxia requires the maintenance of ATP despite the loss of aerobic metabolism in a manner that prevents a disruption of ionic homeostasis. Instead, the abilities to maintain a hypometabolic state with low ATP and tolerate large disturbances in ionic status appear to contribute to the higher anoxia tolerance of adults. Furthermore, metabolomics experiments support this notion by showing that larvae had higher metabolic rates during the initial 30 min of anoxia and that protective metabolites were upregulated in adults but not larvae. Lastly, I investigated the genetic variation in anoxia tolerance using a genome wide association study (GWAS) to identify target genes associated with anoxia tolerance. Results from the GWAS also suggest mechanisms related to protection from ionic and oxidative stress, in addition to a protective role for immune function.
Vertebrate studies suggest that surviving anoxia requires the maintenance of ATP despite the loss of aerobic metabolism in a manner that prevents a disruption of ionic homeostasis. Instead, the abilities to maintain a hypometabolic state with low ATP and tolerate large disturbances in ionic status appear to contribute to the higher anoxia tolerance of adults. Furthermore, metabolomics experiments support this notion by showing that larvae had higher metabolic rates during the initial 30 min of anoxia and that protective metabolites were upregulated in adults but not larvae. Lastly, I investigated the genetic variation in anoxia tolerance using a genome wide association study (GWAS) to identify target genes associated with anoxia tolerance. Results from the GWAS also suggest mechanisms related to protection from ionic and oxidative stress, in addition to a protective role for immune function.
ContributorsCampbell, Jacob B (Author) / Harrison, Jon F. (Thesis advisor) / Gadau, Juergen (Committee member) / Call, Gerald B (Committee member) / Sweazea, Karen L (Committee member) / Rosenberg, Michael S. (Committee member) / Arizona State University (Publisher)
Created2018
Description
Isolation-by-distance is a specific type of spatial genetic structure that arises when parent-offspring dispersal is limited. Many natural populations exhibit localized dispersal, and as a result, individuals that are geographically near each other will tend to have greater genetic similarity than individuals that are further apart. It is important to identify isolation-by-distance because it can impact the statistical analysis of population samples and it can help us better understand evolutionary dynamics. For this dissertation I investigated several aspects of isolation-by-distance. First, I looked at how the shape of the dispersal distribution affects the observed pattern of isolation-by-distance. If, as theory predicts, the shape of the distribution has little effect, then it would be more practical to model isolation-by-distance using a simple dispersal distribution rather than replicating the complexities of more realistic distributions. Therefore, I developed an efficient algorithm to simulate dispersal based on a simple triangular distribution, and using a simulation, I confirmed that the pattern of isolation-by-distance was similar to other more realistic distributions. Second, I developed a Bayesian method to quantify isolation-by-distance using genetic data by estimating Wright’s neighborhood size parameter. I analyzed the performance of this method using simulated data and a microsatellite data set from two populations of Maritime pine, and I found that the neighborhood size estimates had good coverage and low error. Finally, one of the major consequences of isolation-by-distance is an increase in inbreeding. Plants are often particularly susceptible to inbreeding, and as a result, they have evolved many inbreeding avoidance mechanisms. Using a simulation, I determined which mechanisms are more successful at preventing inbreeding associated with isolation-by-distance.
ContributorsFurstenau, Tara N (Author) / Cartwright, Reed A (Thesis advisor) / Rosenberg, Michael S. (Committee member) / Taylor, Jesse (Committee member) / Wilson-Sayres, Melissa (Committee member) / Arizona State University (Publisher)
Created2015
Description
Leprosy and tuberculosis are age-old diseases that have tormented mankind and left behind a legacy of fear, mutilation, and social stigmatization. Today, leprosy is considered a Neglected Tropical Disease due to its high prevalence in developing countries, while tuberculosis is highly endemic in developing countries and rapidly re-emerging in several developed countries. In order to eradicate these diseases effectively, it is necessary to understand how they first originated in humans and whether they are prevalent in nonhuman hosts which can serve as a source of zoonotic transmission. This dissertation uses a phylogenomics approach to elucidate the evolutionary histories of the pathogens that cause leprosy and tuberculosis, Mycobacterium leprae and the M. tuberculosis complex, respectively, through three related studies. In the first study, genomes of M. leprae strains that infect nonhuman primates were sequenced and compared to human M. leprae strains to determine their genetic relationships. This study assesses whether nonhuman primates serve as a reservoir for M. leprae and whether there is potential for transmission of M. leprae between humans and nonhuman primates. In the second study, the genome of M. lepraemurium (which causes leprosy in mice, rats, and cats) was sequenced to clarify its genetic relationship to M. leprae and other mycobacterial species. This study is the first to sequence the M. lepraemurium genome and also describes genes that may be important for virulence in this pathogen. In the third study, an ancient DNA approach was used to recover M. tuberculosis genomes from human skeletal remains from the North American archaeological record. This study informs us about the types of M. tuberculosis strains present in post-contact era North America. Overall, this dissertation informs us about the evolutionary histories of these pathogens and their prevalence in nonhuman hosts, which is not only important in an anthropological context but also has significant implications for disease eradication and wildlife conservation.
ContributorsHonap, Tanvi Prasad (Author) / Stone, Anne C (Thesis advisor) / Rosenberg, Michael S. (Thesis advisor) / Clark-Curtiss, Josephine E (Committee member) / Krause, Johannes (Committee member) / Arizona State University (Publisher)
Created2017
Description
The closer integration of the world economy has yielded many positive benefits including the worldwide diffusion of innovative technologies and efficiency gains following the widening of international markets. However, closer integration also has negative consequences. Specifically, I focus on the ecology and economics of the spread of species and pathogens. I approach the problem using theoretical and applied models in ecology and economics. First, I use a multi-species theoretical network model to evaluate the ability of dispersal to maintain system-level biodiversity and productivity. I then extend this analysis to consider the effects of dispersal in a coupled social-ecological system where people derive benefits from species. Finally, I estimate an empirical model of the foot and mouth disease risks of trade. By combining outbreak and trade data I estimate the disease risks associated with the international trade in live animals while controlling for the biosecurity measures in place in importing countries and the presence of wild reservoirs. I find that the risks associated with the spread and dispersal of species may be positive or negative, but that this relationship depends on the ecological and economic components of the system and the interactions between them.
ContributorsShanafelt, David William (Author) / Perrings, Charles (Thesis advisor) / Fenichel, Eli (Committee member) / Richards, Timorthy (Committee member) / Janssen, Marco (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2016