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MBE Advance Access published online on August 29, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg207
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted June 23, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Analysis of the Evolutionary Relationships of HIV-1 and SIVcpz Sequences Using Bayesian Inference: Implications for the Origin of HIV-1

D. Paraskevis 1, P. Lemey 1, M. Salemi 1, M. Suchard 2, Y. Van der Peer 3, and A.-M. Vandamme 1*

1 Rega Institute for Medical Research, Katholieke Universiteit Leuven, Belgium
2 Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, USA
3 Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Gent University, Belgium

* To whom correspondence should be addressed. E-mail: annemie.vandamme{at}uz.kuleuven.ac.be.


  Abstract

The most plausible origin of HIV-1 group M is an SIV lineage currently represented by SIVcpz isolated from the chimpanzee subspecies P.t.troglodytes. The origin of HIV-1 group O is less clear. Putative recombination between any of the HIV-1 and SIVcpz sequences was tested using boot- and Bayesian-scanning plots, as well as a new method to infer parental sequences and crossing over points using a Bayesian multiple change-point (BMCP) model. We found that in the case of highly divergent sequences, such as HIV-1/SIVcpz, Bayesian scanning and BMCP methods are more appropriate than bootscanning analysis to investigate spatial phylogenetic variation, including estimating the boundaries of the regions with discordant evolutionary relationships, and the levels of support of the phylogenetic clusters under study. According to the Bayesian-scanning plots and BMCP method, there was strong evidence for discordant phylogenetic clustering throughout the genome: 1) HIV-1 group O clustered with SIVcpzANT/TAN in middle pol, and partial vif/env; 2) SIVcpzGab1 clustered with SIVcpzANT/TAN in 3'pol/vif, and middle env, 3) HIV-1 group O grouped with SIVcpzCamUS and SIVcpzGab1 in p17/p24, 4) HIV-1 group M was more closely related to SIVcpzCamUS in 3'gag/pol and in middle pol, whereas in partial gp120 group M clustered with group O. Conditionally independent phylogenetic analysis inferred by maximum likelihood (ML) and Bayesian methods confirmed further these findings. The discordant phylogenetic relationships between the HIV-1/SIVcpz sequences may have been caused by ancient recombination events, but are at least in part also due to altered rates of evolution between parental SIVcpz lineages.

Key Words: HIV, SIVcpz, evolution, Bayesian inference


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