ArticleProceedings of the National Academy of Sciences of the United States of America2006
Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Variations and evolution of HIV-1 provirus in peripheral blood under the pressure of ART.Virus evolution · 2026Article
- Intra-host evolution of cell-fusing agent virus following acute infection inVirus evolution · 2025Article
- Dinucleotide codon substitutions as a signature of diversifying selection inFrontiers in molecular biosciences · 2025Article
- Different Patterns of Codon Usage and Amino Acid Composition across Primate Lentiviruses.Viruses · 2023Article
- Phylogenetic inference of changes in amino acid propensities with single-position resolution.PLoS computational biology · 2022Article
- Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins.PLoS genetics · 2021Article
- Crossing fitness valleys via double substitutions within codons.BMC biology · 2019Article
- High-Sequence Diversity and Rapid Virus Turnover Contribute to Higher Rates of Coreceptor Switching in Treatment-Experienced Subjects with HIV-1 Viremia.AIDS research and human retroviruses · 2017Article
- Coordinated Evolution of Influenza A Surface Proteins.PLoS genetics · 2015Article
- Dendritic cells restore CD8+ T cell reactivity to autologous HIV-1.Journal of virology · 2014Article
- Prevalence of multinucleotide replacements in evolution of primates and Drosophila.Molecular biology and evolution · 2013Article
- The evolutionary significance of certain amino acid substitutions and their consequences for HIV-1 immunogenicity toward HLA's A*0201 and B*27.Bioinformation · 2013Article
- Major role of positive selection in the evolution of conservative segments of Drosophila proteins.Proceedings. Biological sciences · 2012Article
- Weak selection and protein evolution.Genetics · 2012Review
- Correlated evolution of nearby residues in Drosophilid proteins.PLoS genetics · 2011Article
- Prevalence of epistasis in the evolution of influenza A surface proteins.PLoS genetics · 2011Article
- Recombination rate and selection strength in HIV intra-patient evolution.PLoS computational biology · 2010Article
- Polymorphism due to multiple amino acid substitutions at a codon site within Ciona savignyi.Genetics · 2009Article
- Dynamic features of the selective pressure on the human immunodeficiency virus type 1 (HIV-1) gp120 CD4-binding site in a group of long term non progressor (LTNP) subjects.Retrovirology · 2009Article
- Genetic diversity in the SIR model of pathogen evolution.PloS one · 2009Article
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4 authors.
Funding
Abstract
The fixation of a new allele can be driven by Darwinian positive selection or can be due to random genetic drift. Identifying instances of positive selection is a difficult task, because its impact is routinely obscured by the action of negative selection. The nature of the genetic code dictates that positive selection in favor of an amino acid replacement should often cause a burst of two or three nucleotide substitutions at a single codon site, because a large fraction of amino acid replacements cannot be achieved after just one nucleotide substitution. Here, we study pairs of successive nonsynonymous substitutions at one codon in the course of evolution of HIV-1 genes within HIV-1 populations inhabiting infected individuals. Such pairs are more numerous and more clumped than expected if different substitutions were independent and than what is observed for pairs of successive synonymous substitutions. Bursts of nonsynonymous substitutions in HIV-1 evolution cannot be explained by mutational biases and must, therefore, be due to positive selection. Both reversals, exact or imprecise, of fixed deleterious mutations and acquisitions of amino acids with new properties are responsible for the bursts. Temporal clumping is strongest at codon sites with a low overall rate of nonsynonymous evolution, implying that a substantial fraction of replacements of conservative amino acids are driven by positive selection. We identified many conservative sites of HIV-1 proteins that occasionally experience positive selection.
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