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Title: Short-term and long-term evolution of lentiviruses
Author: Li, Li
Awarding Body: University of Nottingham
Current Institution: University of Nottingham
Date of Award: 2011
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Lentiviruses have paradoxically fast short-term rate of evolution and slow long-term rate of evolution, which differ by several orders of magnitude. In this thesis, with a new method called truncated tree analysis, slower rates of evolution of transmitted viruses were estimated. However, the rate decline of the transmitted viruses is limited, and is not sufficient to explain the dramatic difference between the short-term and long-term evolutionary rates. These dramatically different rates were reconciled by an S shaped curve based on the new trend observed from this thesis. In the middle part of this new trend, the rate of evolution decreases as the time of divergence increases. Using this new trend, the time scale of HIV -1 and their closest related SIV found in apes were set. The SIV cpzPtt and SIV cpzPts isolated from the two subspecies of chimpanzees shared the most recent common ancestor around 25.2 thousand years ago. This is younger than the estimated date of these two host subspecies split, and suggests that the SIV cpz is relatively new to the chimpanzees. The second chapter of this thesis further explores lentiviral evolution by examining the feline immunodeficiency viruses (FIV's). An American origin scenario of the FIV s was proposed. In this scenario the ancestor of FIV first the invaded the ancestors of the puma lineage living in American, and then as the ancient puma lineage speciated and migrated FIV spread out to many other felids. The final chapter of this thesis further explores the evolutionary rate decline as the time span extends by introducing the idea of flip- flop sites that undergo negative frequency dependent selection pressures. Theoretical simulations confirmed that in the short time span, the presence of the flip-flop sites results in overestimation of the evolutionary rate, but in longer time spans, opposite effects of flip-flop sites were observed.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available