Host structuring of parasite populations: Some theoretical and computational studies

Persistent Link:
http://hdl.handle.net/10150/289991
Title:
Host structuring of parasite populations: Some theoretical and computational studies
Author:
Taylor, Jesse Earl
Issue Date:
2003
Publisher:
The University of Arizona.
Rights:
Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
Abstract:
Because the ecological and the genetic interactions occurring between parasites belonging to different infections are constrained by the physical discreteness of the hosts, the host-parasite association imparts a spatial structure to the populations of parasitic microorganisms. Equating infections with demes or islands, the parasite population can be described by a variant of Wright's island model, in which recovery and infection correspond to extinction and colonization and superinfection corresponds to migration. Here we investigate some of the population genetic consequences of host structure using a combination of theoretical and computational methods. In our first study, we introduce a measure-valued process as a model for the evolution of an age-structured parasite metapopulation and show how to approximate this process using the measure flow generated by a jump-diffusion. We characterize the invariant measures and corresponding jump distributions for the approximation and apply these methods to an example involving a single locus subject to mutation, selection, and genetic drift within hosts and to bottlenecks and bias during transmission. When intrahost selection and transmission bias act discordantly, it is shown that the invariant measure and the jump distribution can differ substantially. We discuss the implications of such discordance for vaccine target selection and review the evidence for biased transmission of HIV-1. In our second study, we use a branching Fisher-Wright process to characterize diversity in an exponentially expanding epidemic. We derive a renewal equation for the persistence probability of the branching diffusion and show that with sufficiently rapid branching a set of k neutral alleles can persist indefinitely with positive probability. In the last study, we exploit the relationship between population recombination rates and superinfection rates to quantify intra-subtype superinfection by HIV-1 in populations from Africa, China, Thailand, Trinidad and Tobago, and the US. Comparison of the population recombination rates estimated for these data sets with those found for data sets simulated using a structured coalescent process representing HIV-1 evolution within an epidemiologically closed population indicates that per-sequence superinfection rates are probably not less than 15% of the corresponding infection rates.
Type:
text; Dissertation-Reproduction (electronic)
Keywords:
Biology, Genetics.; Health Sciences, Immunology.
Degree Name:
Ph.D.
Degree Level:
doctoral
Degree Program:
Graduate College; Ecology and Evolutionary Biology
Degree Grantor:
University of Arizona
Advisor:
Walsh, Bruce

Full metadata record

DC FieldValue Language
dc.language.isoen_USen_US
dc.titleHost structuring of parasite populations: Some theoretical and computational studiesen_US
dc.creatorTaylor, Jesse Earlen_US
dc.contributor.authorTaylor, Jesse Earlen_US
dc.date.issued2003en_US
dc.publisherThe University of Arizona.en_US
dc.rightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.en_US
dc.description.abstractBecause the ecological and the genetic interactions occurring between parasites belonging to different infections are constrained by the physical discreteness of the hosts, the host-parasite association imparts a spatial structure to the populations of parasitic microorganisms. Equating infections with demes or islands, the parasite population can be described by a variant of Wright's island model, in which recovery and infection correspond to extinction and colonization and superinfection corresponds to migration. Here we investigate some of the population genetic consequences of host structure using a combination of theoretical and computational methods. In our first study, we introduce a measure-valued process as a model for the evolution of an age-structured parasite metapopulation and show how to approximate this process using the measure flow generated by a jump-diffusion. We characterize the invariant measures and corresponding jump distributions for the approximation and apply these methods to an example involving a single locus subject to mutation, selection, and genetic drift within hosts and to bottlenecks and bias during transmission. When intrahost selection and transmission bias act discordantly, it is shown that the invariant measure and the jump distribution can differ substantially. We discuss the implications of such discordance for vaccine target selection and review the evidence for biased transmission of HIV-1. In our second study, we use a branching Fisher-Wright process to characterize diversity in an exponentially expanding epidemic. We derive a renewal equation for the persistence probability of the branching diffusion and show that with sufficiently rapid branching a set of k neutral alleles can persist indefinitely with positive probability. In the last study, we exploit the relationship between population recombination rates and superinfection rates to quantify intra-subtype superinfection by HIV-1 in populations from Africa, China, Thailand, Trinidad and Tobago, and the US. Comparison of the population recombination rates estimated for these data sets with those found for data sets simulated using a structured coalescent process representing HIV-1 evolution within an epidemiologically closed population indicates that per-sequence superinfection rates are probably not less than 15% of the corresponding infection rates.en_US
dc.typetexten_US
dc.typeDissertation-Reproduction (electronic)en_US
dc.subjectBiology, Genetics.en_US
dc.subjectHealth Sciences, Immunology.en_US
thesis.degree.namePh.D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.disciplineGraduate Collegeen_US
thesis.degree.disciplineEcology and Evolutionary Biologyen_US
thesis.degree.grantorUniversity of Arizonaen_US
dc.contributor.advisorWalsh, Bruceen_US
dc.identifier.proquest3108960en_US
dc.identifier.bibrecord.b44830762en_US
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