Matching Items (30)
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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

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
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Description
Using a simple $SI$ infection model, I uncover the

overall dynamics of the system and how they depend on the incidence

function. I consider both an epidemic and endemic perspective of the

model, but in both cases, three classes of incidence

functions are identified.

In the epidemic form,

power incidences, where the infective portion $I^p$

Using a simple $SI$ infection model, I uncover the

overall dynamics of the system and how they depend on the incidence

function. I consider both an epidemic and endemic perspective of the

model, but in both cases, three classes of incidence

functions are identified.

In the epidemic form,

power incidences, where the infective portion $I^p$ has $p\in(0,1)$,

cause unconditional host extinction,

homogeneous incidences have host extinction for certain parameter constellations and

host survival for others, and upper density-dependent incidences

never cause host extinction. The case of non-extinction in upper

density-dependent

incidences extends to the case where a latent period is included.

Using data from experiments with rhanavirus and salamanders,

maximum likelihood estimates are applied to the data.

With these estimates,

I generate the corrected Akaike information criteria, which

reward a low likelihood and punish the use of more parameters.

This generates the Akaike weight, which is used to fit

parameters to the data, and determine which incidence functions

fit the data the best.

From an endemic perspective, I observe

that power incidences cause initial condition dependent host extinction for

some parameter constellations and global stability for others,

homogeneous incidences have host extinction for certain parameter constellations and

host survival for others, and upper density-dependent incidences

never cause host extinction.

The dynamics when the incidence function is homogeneous are deeply explored.

I expand the endemic considerations in the homogeneous case

by adding a predator into the model.

Using persistence theory, I show the conditions for the persistence of each of the

predator, prey, and parasite species. Potential dynamics of the system include parasite mediated

persistence of the predator, survival of the ecosystem at high initial predator levels and

ecosystem collapse at low initial predator levels, persistence of all three species, and much more.
ContributorsFarrell, Alexander E. (Author) / Thieme, Horst R (Thesis advisor) / Smith, Hal (Committee member) / Kuang, Yang (Committee member) / Tang, Wenbo (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2017
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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

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
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Description
The Committee on Rare and Endangered Wildlife Species (CREWS) of the U.S. Fish and Wildlife Service (FWS) made important and lasting contributions to one of the most significant pieces of environmental legislation in U.S. history: the Endangered Species Act of 1973 (ESA). CREWS was a prominent science-advisory body within the

The Committee on Rare and Endangered Wildlife Species (CREWS) of the U.S. Fish and Wildlife Service (FWS) made important and lasting contributions to one of the most significant pieces of environmental legislation in U.S. history: the Endangered Species Act of 1973 (ESA). CREWS was a prominent science-advisory body within the U.S. Department of the Interior (DOI) in the 1960s and 1970s, responsible for advising on the development of federal endangered-wildlife policy. The Committee took full advantage of its scientific and political authority by identifying a particular object of conservation--used in the development of the first U.S. list of endangered species--and establishing captive breeding as a primary conservation practice, both of which were written into the ESA and are employed in endangered-species listing and recovery to this day. Despite these important contributions to federal endangered-species practice and policy, CREWS has received little attention from historians of science or policy scholars. This dissertation is an empirical history of CREWS that draws on primary sources from the Smithsonian Institution (SI) Archives and a detailed analysis of the U.S. congressional record. The SI sources (including the records of the Bird and Mammal Laboratory, an FWS staffed research group stationed at the Smithsonian Institution) reveal the technical and political details of CREWS's advisory work. The congressional record provides evidence showing significant contributions of CREWS and its advisors and supervisors to the legislative process that resulted in the inclusion of key CREWS-inspired concepts and practices in the ESA. The foundational concepts and practices of the CREWS's research program drew from a number of areas currently of interest to several sub-disciplines that investigate the complex relationship between science and society. Among them are migratory bird conservation, systematics inspired by the Evolutionary Synthesis, species-focused ecology, captive breeding, reintroduction, and species transplantation. The following pages describe the role played by CREWS in drawing these various threads together and codifying them as endangered-species policy in the ESA.
ContributorsWinston, Johnny (Author) / Hamilton, Andrew (Thesis advisor) / Maienschein, Jane (Committee member) / Henson, Pamela (Committee member) / Collins, James (Committee member) / Minteer, Ben (Committee member) / Arizona State University (Publisher)
Created2011
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Description

Today, some modern zoos, aquariums, and similar animal-exhibiting institutions continue to shift their priorities toward a focus on the conservation of wildlife. Conservation challenges span a broad subject area. The focus that any institution chooses can vary greatly in terms of magnitude and measures of significance. Many modern zoos often

Today, some modern zoos, aquariums, and similar animal-exhibiting institutions continue to shift their priorities toward a focus on the conservation of wildlife. Conservation challenges span a broad subject area. The focus that any institution chooses can vary greatly in terms of magnitude and measures of significance. Many modern zoos often choose to make global conservation a central institutional priority: conservation of biodiversity, habitat protection, species extinction, and more. Some institutions, however, set conservation priorities on a smaller scale, focusing on contributions that have a more indirect effect on wild species and habitats, such as the welfare of populations in captivity, raising public awareness of conservation missions, and conservation education. By comparing the institutional priorities of two organizations within the Association of Zoos and Aquariums (AZA), the Arizona-Sonora Desert Museum and the Phoenix Zoo, I explore how each institution manages its living collections and works toward its respective conservation mission. I interviewed members of each institution and analyzed the similarities and differences between the organizations based on their management of living collections, and how different mission statements might shape their work. This included investigating the focus each institution has on animal welfare, in situ and ex situ conservation, and maintaining public interest. This also required defining what conservation and welfare mean to each institution and how that affects the management of their living collections. From a literature review and interviews with representatives from each institution, I was able to determine that despite any differences in style or in the language of respective mission statements, each institution prioritizes connecting the public and conservation of biodiversity. While they employ different approaches - one institution takes a regional interest in the Sonoran Desert ecosystem and landscape; the other takes a more global approach to its experiences, exhibits, and collections - the core values and ultimately the vision remain the same. Conservation may serve as the primary motivator for both the Museum and the Zoo, but my thesis is that this rationale could not be realized by itself for these institutions. Rather, conservation as a core value relies upon the support of other critical institutional priorities working together. In this way animal welfare, public engagement, and conservation relate to one another as institutional values and create the impact that the zoo and museum have on their local communities, as well as on conservation as a whole.

ContributorsOlson, Ellyse (Author) / Collins, James (Thesis director) / Minteer, Ben (Committee member) / School of Community Resources and Development (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

As zoos’ goals, designers’ values, and guests’ expectations change, so do the structures seen at the zoo. Exhibit history is not clear cut, and – despite what some may claim – is not inherently linear. Exhibit strategies develop as a result of tensions, both social and operational, imposed from both

As zoos’ goals, designers’ values, and guests’ expectations change, so do the structures seen at the zoo. Exhibit history is not clear cut, and – despite what some may claim – is not inherently linear. Exhibit strategies develop as a result of tensions, both social and operational, imposed from both inside and outside of zoos. This literature review examines the history of zoo architecture by defining six design periods and considering the lenses of race, class, and nature.

ContributorsBisgrove, Daniel Jeffrey (Author) / Minteer, Ben (Thesis director) / Collins, James (Committee member) / Rojas, Christopher (Committee member) / School of Community Resources and Development (Contributor) / School of Life Sciences (Contributor, Contributor, Contributor, Contributor) / Division of Teacher Preparation (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description
Evolution is a key feature of undergraduate biology education: the AmericanAssociation for the Advancement of Science (AAAS) has identified evolution as one of the five core concepts of biology, and it is relevant to a wide array of biology-related careers. If biology instructors want students to use evolution to address scientific challenges post-graduation,

Evolution is a key feature of undergraduate biology education: the AmericanAssociation for the Advancement of Science (AAAS) has identified evolution as one of the five core concepts of biology, and it is relevant to a wide array of biology-related careers. If biology instructors want students to use evolution to address scientific challenges post-graduation, students need to be able to apply evolutionary principles to real-life situations, and accept that the theory of evolution is the best scientific explanation for the unity and diversity of life on Earth. In order to help students progress on both fronts, biology education researchers need surveys that measure evolution acceptance and assessments that measure students’ ability to apply evolutionary concepts. This dissertation improves the measurement of student understanding and acceptance of evolution by (1) developing a novel Evolutionary Medicine Assessment that measures students’ ability to apply the core principles of Evolutionary Medicine to a variety of health-related scenarios, (2) reevaluating existing measures of student evolution acceptance by using student interviews to assess response process validity, and (3) correcting the validity issues identified on the most widely-used measure of evolution acceptance - the Measure of Acceptance of the Theory of Evolution (MATE) - by developing and validating a revised version of this survey: the MATE 2.0.
ContributorsMisheva, Anastasia Taya (Author) / Brownell, Sara (Thesis advisor) / Barnes, Elizabeth (Committee member) / Collins, James (Committee member) / Cooper, Katelyn (Committee member) / Sterner, Beckett (Committee member) / Arizona State University (Publisher)
Created2023
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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

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.
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
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Description
Insecticide resistance is a continuing issue that negatively affects both public health and agriculture and allows vector-borne diseases to spread throughout the globe. To improve resistance management strategies (RMS), robust susceptibility bioassays need to be performed in order to fill the gap of the relationship between resistant and susceptible genotype

Insecticide resistance is a continuing issue that negatively affects both public health and agriculture and allows vector-borne diseases to spread throughout the globe. To improve resistance management strategies (RMS), robust susceptibility bioassays need to be performed in order to fill the gap of the relationship between resistant and susceptible genotype and phenotype, and a deeper knowledge of how bioassay data relates to vector control success or failure is imperative. A bioassay method that is infrequently used but yields robust results is the topical application bioassay, where the insect is directly treated with a constant volume and concentration of an insecticide via a syringe. To bring more attention to this method, my colleagues and I published a paper in the Journal of Visualized Experiments where the optimized protocol of the topical application bioassay for mosquitoes and fruit flies is described, and the strengths and limitations to the method are explained. To further investigate insecticide susceptibility tests, I set up my individual project where I used Aedes aegypti mosquitoes to compare the topical application bioassay to the commonly used Centers for Disease Control and Prevention (CDC) bottle bioassay and World Health Organization (WHO) tube test. The objective of this study was to test which method exhibited the most variability in mortality results, which would guide the choice of assay to determine the link between resistant and susceptible genotype and phenotype. The results showed that the topical application method did indeed exhibit the least amount of variation, followed by the CDC bottle bioassay (WHO data is currently being collected). This suggests that the topical application bioassay could be a useful tool in insecticide resistance surveillance studies, and, depending on the goal, may be better than the CDC and WHO tube tests for assessing resistance levels at a given site. This study challenges the value of the widely used CDC and WHO assays and provides a discussion on the importance of technical and practical resistance assays. This will help vector control specialists to collect accurate surveillance data that will inform effective RMS.
ContributorsAlthoff, Rachel (Author) / Huijben, Silvie (Thesis advisor) / Harris, Robin (Committee member) / Collins, James (Committee member) / Arizona State University (Publisher)
Created2022
Description
The use of genetic management in conservation has sparked much debate around the ethical and environmental impacts of the plans. A case study on the conservation of leopard frogs in Arizona was analyzed to better understand the benefits and issues surrounding genetic management plans. The first part of the case

The use of genetic management in conservation has sparked much debate around the ethical and environmental impacts of the plans. A case study on the conservation of leopard frogs in Arizona was analyzed to better understand the benefits and issues surrounding genetic management plans. The first part of the case focuses on the recent management plan for Chiricahua Leopard Frogs implemented by the Arizona Game and Fish Department. The goal of the plan is to better understand the genetic dynamics of the established Chiricahua Leopard Frog populations to develop a more effective management plan. The second part of the case focuses on the Arizona Game and Fish Department’s management of the Northern Leopard Frog. There was little success with the initial breed and release program of the native species, however a nonnative subspecies of Northern Leopard Frog was able to establish a thriving population. This case study exemplifies the many complications with genetic management plans and the importance of careful assessment of options when deciding on a genetic management plan. Despite the complexity of genetic management plans, it is an important method to consider when discussing the conservation of a species.
ContributorsTurpen, Alexa (Author) / Murphree, Julie (Thesis director) / Collins, James (Thesis director) / Owens, Audrey (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / College of Integrative Sciences and Arts (Contributor) / School of Mathematical and Natural Sciences (Contributor)
Created2024-05