Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
Displaying 1 - 4 of 4
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- All Subjects: Ecology
- All Subjects: Plasmodium
Description
In complex consumer-resource type systems, where diverse individuals are interconnected and interdependent, one can often anticipate what has become known as the tragedy of the commons, i.e., a situation, when overly efficient consumers exhaust the common resource, causing collapse of the entire population. In this dissertation I use mathematical modeling to explore different variations on the consumer-resource type systems, identifying some possible transitional regimes that can precede the tragedy of the commons. I then reformulate it as a game of a multi-player prisoner's dilemma and study two possible approaches for preventing it, namely direct modification of players' payoffs through punishment/reward and modification of the environment in which the interactions occur. I also investigate the questions of whether the strategy of resource allocation for reproduction or competition would yield higher fitness in an evolving consumer-resource type system and demonstrate that the direction in which the system will evolve will depend not only on the state of the environment but largely on the initial composition of the population. I then apply the developed framework to modeling cancer as an evolving ecological system and draw conclusions about some alternative approaches to cancer treatment.
ContributorsKareva, Irina (Author) / Castillo-Chavez, Carlos (Thesis advisor) / Collins, James (Committee member) / Nagy, John (Committee member) / Smith, Hal (Committee member) / Arizona State University (Publisher)
Created2012
Description
The complex life cycle and widespread range of infection of Plasmodium parasites, the causal agent of malaria in humans, makes them the perfect organism for the study of various evolutionary mechanisms. In particular, multigene families are considered one of the main sources for genome adaptability and innovation. Within Plasmodium, numerous species- and clade-specific multigene families have major functions in the development and maintenance of infection. Nonetheless, while the evolutionary mechanisms predominant on many species- and clade-specific multigene families have been previously studied, there are far less studies dedicated to analyzing genus common multigene families (GCMFs). I studied the patterns of natural selection and recombination in 90 GCMFs with diverse numbers of gene gain/loss events. I found that the majority of GCMFs are formed by duplications events that predate speciation of mammal Plasmodium species, with many paralogs being neutrally maintained thereafter. In general, multigene families involved in immune evasion and host cell invasion commonly showed signs of positive selection and species-specific gain/loss events; particularly, on Plasmodium species is the simian and rodent clades. A particular multigene family: the merozoite surface protein-7 (msp7) family, is found in all Plasmodium species and has functions related to the erythrocyte invasion. Within Plasmodium vivax, differences in the number of paralogs in this multigene family has been previously explained, at least in part, as potential adaptations to the human host. To investigate this I studied msp7 orthologs in closely related non-human primate parasites where homology was evident. I also estimated paralogs’ evolutionary history and genetic polymorphism. The emerging patterns where compared with those of Plasmodium falciparum. I found that the evolution of the msp7 multigene family is consistent with a Birth-and-Death model where duplications, pseudogenization and gene lost events are common. In order to study additional aspects in the evolution of Plasmodium, I evaluated the trends of long term and short term evolution and the putative effects of vertebrate- host’s immune pressure of gametocytes across various Plasmodium species. Gametocytes, represent the only sexual stage within the Plasmodium life cycle, and are also the transition stages from the vertebrate to the mosquito vector. I found that, while male and female gametocytes showed different levels of immunogenicity, signs of positive selection were not entirely related to the location and presence of immune epitope regions. Overall, these studies further highlight the complex evolutionary patterns observed in Plasmodium.
ContributorsCastillo Siri, Andreina I (Author) / Rosenberg, Michael (Thesis advisor) / Escalante, Ananias (Committee member) / Taylor, Jesse (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2016
Description
How fast is evolution? In this dissertation I document a profound change that occurred around the middle of the 20th century in the way that ecologists conceptualized the temporal and spatial scales of adaptive evolution, through the lens of British plant ecologist Anthony David Bradshaw (1926–2008). In the early 1960s, one prominent ecologist distinguished what he called “ecological time”—around ten generations—from “evolutionary time”— around half of a million years. For most ecologists working in the first half of the 20th century, evolution by natural selection was indeed a slow and plodding process, tangible in its products but not in its processes, and inconsequential for explaining most ecological phenomena. During the 1960s, however, many ecologists began to see evolution as potentially rapid and observable. Natural selection moved from the distant past—a remote explanans for both extant biological diversity and paleontological phenomena—to a measurable, quantifiable mechanism molding populations in real time.
The idea that adaptive evolution could be rapid and highly localized was a significant enabling condition for the emergence of ecological genetics in the second half of the 20th century. Most of what historians know about that conceptual shift and the rise of ecological genetics centers on the work of Oxford zoologist E. B. Ford and his students on polymorphism in Lepidotera, especially industrial melanism in Biston betularia. I argue that ecological genetics in Britain was not the brainchild of an infamous patriarch (Ford), but rather the outgrowth of a long tradition of pastureland research at plant breeding stations in Scotland and Wales, part of a discipline known as “genecology” or “experimental taxonomy.” Bradshaw’s investigative activities between 1948 and 1968 were an outgrowth of the specific brand of plant genecology practiced at the Welsh and Scottish Plant Breeding stations. Bradshaw generated evidence that plant populations with negligible reproductive isolation—separated by just a few meters—could diverge and adapt to contrasting environmental conditions in just a few generations. In Bradshaw’s research one can observe the crystallization of a new concept of rapid adaptive evolution, and the methodological and conceptual transformation of genecology into ecological genetics.
The idea that adaptive evolution could be rapid and highly localized was a significant enabling condition for the emergence of ecological genetics in the second half of the 20th century. Most of what historians know about that conceptual shift and the rise of ecological genetics centers on the work of Oxford zoologist E. B. Ford and his students on polymorphism in Lepidotera, especially industrial melanism in Biston betularia. I argue that ecological genetics in Britain was not the brainchild of an infamous patriarch (Ford), but rather the outgrowth of a long tradition of pastureland research at plant breeding stations in Scotland and Wales, part of a discipline known as “genecology” or “experimental taxonomy.” Bradshaw’s investigative activities between 1948 and 1968 were an outgrowth of the specific brand of plant genecology practiced at the Welsh and Scottish Plant Breeding stations. Bradshaw generated evidence that plant populations with negligible reproductive isolation—separated by just a few meters—could diverge and adapt to contrasting environmental conditions in just a few generations. In Bradshaw’s research one can observe the crystallization of a new concept of rapid adaptive evolution, and the methodological and conceptual transformation of genecology into ecological genetics.
ContributorsPeirson, Bruce Richard Erick (Author) / Laubichler, Manfred D (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Creath, Richard (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2015
Description
Evaluations of chemical energy supplies for redox reactions used by chemotrophs in water-rock hosted ecosystems are often done separately from evaluations of chemotroph diversity. However, given that energy is a fundamental and unifying parameter for life, much can be gained by evaluating chemical energy as an ecological parameter of water-rock hosted ecosystems. Therefore, I developed an approach that combines evaluation of chemical energy supplies with 16S and 18S rRNA gene amplicon sequencing. I used this approach to assess drivers of microbial distribution, diversity and activity in serpentinized fluids of the Samail Ophiolite of Oman and in hot springs in Yellowstone National Park.
Through the application of the approach, microbiological interactions in serpentinized fluids were found to be more complex than anticipated. Serpentinized fluids are hyperalkaline and pH is often considered the driving parameter of microbial diversity, however hydrogenotrophic community composition varies in hyperalkaline fluids with similar pH. The composition of hydrogenotrophic communities in serpentinized fluids were found to correspond to the availability of the electron acceptor for hydrogenotrophic redox reactions. Specifically, hydrogenotrophic community composition transitions from being dominated by the hydrogenotrophic methanogen genus, Methanobacterium, when the concentration of sulfate is less than ~10 μm. Above ~10 μm, sulfate reducers are most abundant. Additionally, Methanobacterium was found to co-occur with the protist genus, Cyclidium, in serpentinized fluids. Species of Cyclidium are anaerobic and known to have methanogen endosymbionts. Therefore, Cyclidium may supply inorganic carbon evolved from fermentation to Methanobacterium, thereby mitigating pH dependent inorganic carbon limitation.
This approach also revealed possible biological mechanisms for methane oxidation in Yellowstone hot springs. Measurable rates of biological methane oxidation in hot spring sediments are likely associated with methanotrophs of the phylum, Verrucomicrobia, and the class, Alphaproteobacteria. Additionally, rates were measurable where known methanotrophs were not detected. At some of these sites, archaeal ammonia oxidizer taxa were detected. Ammonia oxidizers have been shown to be capable of methane oxidation in other systems and may be an alternative mechanism for methanotrophy in Yellowstone hot springs. At the remaining sites, uncharacterized microbial lineages may be capable of carrying out methane oxidation in Yellowstone hot springs.
Through the application of the approach, microbiological interactions in serpentinized fluids were found to be more complex than anticipated. Serpentinized fluids are hyperalkaline and pH is often considered the driving parameter of microbial diversity, however hydrogenotrophic community composition varies in hyperalkaline fluids with similar pH. The composition of hydrogenotrophic communities in serpentinized fluids were found to correspond to the availability of the electron acceptor for hydrogenotrophic redox reactions. Specifically, hydrogenotrophic community composition transitions from being dominated by the hydrogenotrophic methanogen genus, Methanobacterium, when the concentration of sulfate is less than ~10 μm. Above ~10 μm, sulfate reducers are most abundant. Additionally, Methanobacterium was found to co-occur with the protist genus, Cyclidium, in serpentinized fluids. Species of Cyclidium are anaerobic and known to have methanogen endosymbionts. Therefore, Cyclidium may supply inorganic carbon evolved from fermentation to Methanobacterium, thereby mitigating pH dependent inorganic carbon limitation.
This approach also revealed possible biological mechanisms for methane oxidation in Yellowstone hot springs. Measurable rates of biological methane oxidation in hot spring sediments are likely associated with methanotrophs of the phylum, Verrucomicrobia, and the class, Alphaproteobacteria. Additionally, rates were measurable where known methanotrophs were not detected. At some of these sites, archaeal ammonia oxidizer taxa were detected. Ammonia oxidizers have been shown to be capable of methane oxidation in other systems and may be an alternative mechanism for methanotrophy in Yellowstone hot springs. At the remaining sites, uncharacterized microbial lineages may be capable of carrying out methane oxidation in Yellowstone hot springs.
ContributorsHowells, Alta Emily Gessner (Author) / Shock, Everett (Thesis advisor) / Collins, James (Committee member) / Anbar, Ariel (Committee member) / Cadillo-Quiroz, Hinsby (Committee member) / Arizona State University (Publisher)
Created2020