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Type of Document	Dissertation
Author	Forster, Robert Burke
Author's Email Address	forster AT caltech.edu
URN	etd-04262006-231415
Persistent URL	http://resolver.caltech.edu/CaltechETD:etd-04262006-231415
Title	Population dynamics in the presence of quasispecies effects and changing environments
Degree	PhD
Option	Physics
Advisory Committee	Advisor Name Title Christoph Adami Committee Chair Emlyn Willard Hughes Committee Member Mark B. Wise Committee Member Niles Pierce Committee Member
Keywords	chaos quasispecies periodic environment frequency-dependent selection RNA secondary structure population dynamics
Date of Defense	2006-04-21
Availability	unrestricted
Abstract This thesis explores how natural selection acts on organisms such as viruses that have either highly error-prone reproduction or face variable environmental conditions or both. By modeling population dynamics under these conditions, we gain a better understanding of the selective forces at work, both in our simulations and hopefully also in real organisms. With an understanding of the important factors in natural selection we can forecast not only the immediate fate of an existing population but also in what directions such a population might evolve in the future. We demonstrate that the concept of a quasispecies is relevant to evolution in a neutral fitness landscape. Motivated by RNA viruses such as HIV, we use RNA secondary structure as our model system and find that quasispecies effects arise both rapidly and in realistically small populations. We discover that the evolutionary effects of neutral drift, punctuated equilibrium and the selection for mutational robustness extend to the concept of a quasispecies. In our study of periodic environments, we consider the tradeoffs faced by quasispecies in adapting to environmental change. We develop an analytical model to predict whether evolution favors short-term or long-term adaptation and validate our model through simulation. Our results bear directly on the population dynamics of viruses such as West Nile that alternate between two host species. More generally, we discover that a selective pressure exists under these conditions to fuse or split genes with complementary environmental functions. Lastly, we study the general effects of frequency-dependent selection on two strains competing in a periodic environment. Under very general assumptions, we prove that stable coexistence rather than extinction is the likely outcome. The population dynamics of this system may be as simple as stable equilibrium or as complex as deterministic chaos.
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