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MBE Advance Access published online on January 5, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi078
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Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2005; all rights reserved.
Accepted January 3, 2005

Research Article

Evolutionary Dynamics of Human Retroviruses Investigated Through Full Genome Scanning

Philippe Lemey 1*, Sonia Van Dooren 1, and Anne-Mieke Vandamme 1

1 Rega Institute for Medical Research, KULeuven, B-3000 Leuven, Belgium

* To whom correspondence should be addressed.
Philippe Lemey, E-mail: philippe.lemey{at}uz.kuleuven.ac.be


  Abstract

To test hypotheses on the differences in retroviral genetic diversity, we compared the evolutionary dynamics of the Human Immunodeficiency Virus type 1 (HIV-1) group M and the Primate T-cell lymphotropic Virus (PTLV) using a full genome analysis. Evolutionary rates and nonsynonymous/synonymous substitution rate ratios were estimated across the genome using a maximum likelihood sliding window approach and molecular clock properties were investigated. We confirm a remarkable difference in genetic stability and selective pressure at the inter-host level. While there is evidence for adaptive evolution in HIV-1, the evolution of PTLV is almost exclusively characterized by negative selection or nearly neutral processes. For both retroviruses, evolutionary rate estimates across the genome reflect the differential selective constraints. However, based on the relationship between evolutionary rate and selective pressure and based on the comparison of synonymous substitution rates, the differences in rate between HIV-1 and PTLV cannot be explained by selective forces only. Several evolutionary and statistical assumptions, examined using a Bayesian coalescent method, were shown to have little influence on our inference.

Keywords: HIV; HTLV; retrovirus; evolutionary rate; natural selection.
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