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- All Subjects: Evolution
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
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.
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
Description
This thesis contains three chapters, all of which involve using culturally inclusive education to explore the experiences of religious undergraduate biology students. The first chapter is an essay entitled "Toward Culturally Inclusive Undergraduate Biology Education," which describes a literature review performed with the aim of characterizing the landscape of cultural competence and related terms for biology educators and biology education researchers. This chapter highlights the use of 16 different terms related to cultural competence and presents these terms, their definitions, and highlights their similarities and differences. This chapter also identifies gaps in the cultural competence literature, and presents a set of recommendations to support better culturally inclusive interventions in undergraduate science education. The second chapter, entitled "Different Evolution Acceptance Instruments Lead to Different Research Findings," describes a study in which the source of 30 years of conflicting research on the relationship between evolution acceptance and evolution understanding was determined. The results of this study showed that different instruments used to measure evolution acceptance sometimes lead to different research results and conclusions. The final chapter, entitled "Believing That Evolution is Atheistic is Associated with Poor Evolution Education Outcomes Among Religious College Students," describes a study characterizing definitions of evolution that religious undergraduate biology students may hold, and examines the impact that those definitions of evolution have on multiple outcome variables. In this study, we found that among the most religious students, those who thought evolution is atheistic were less accepting of evolution, less comfortable learning evolution, and perceived greater conflict between their personal religious beliefs and evolution than those who thought evolution is agnostic.
ContributorsDunlop, Hayley Marie (Author) / Brownell, Sara (Thesis director) / Collins, James (Committee member) / Barnes, M. Elizabeth (Committee member) / School of Human Evolution & Social Change (Contributor) / School of Life Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2019-05