The evolution of HIV: Inferences using phylogenetics

Eduardo Castro-Nallar, Marcos Pérez-Losada, Gregory F. Burton, Keith A. Crandall

Research output: Contribution to journalReview articlepeer-review

56 Citations (Scopus)


Molecular phylogenetics has revolutionized the study of not only evolution but also disparate fields such as genomics, bioinformatics, epidemiology, ecology, microbiology, molecular biology and biochemistry. Particularly significant are its achievements in population genetics as a result of the development of coalescent theory, which have contributed to more accurate model-based parameter estimation and explicit hypothesis testing. The study of the evolution of many microorganisms, and HIV in particular, have benefited from these new methodologies. HIV is well suited for such sophisticated population analyses because of its large population sizes, short generation times, high substitution rates and relatively small genomes. All these factors make HIV an ideal and fascinating model to study molecular evolution in real time. Here we review the significant advances made in HIV evolution through the application of phylogenetic approaches. We first examine the relative roles of mutation and recombination on the molecular evolution of HIV and its adaptive response to drug therapy and tissue allocation. We then review some of the fundamental questions in HIV evolution in relation to its origin and diversification and describe some of the insights gained using phylogenies. Finally, we show how phylogenetic analysis has advanced our knowledge of HIV dynamics (i.e., phylodynamics).

Original languageEnglish
Pages (from-to)777-792
Number of pages16
JournalMolecular Phylogenetics and Evolution
Issue number2
Publication statusPublished - Feb 2012


  • Drug resistance
  • HIV
  • HIV origins
  • Molecular epidemiology
  • Phylodynamics
  • Phylogenetics
  • Reservoir
  • Vaccine resistance
  • Viral transmission
  • Virus evolution

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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