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Related Concept Videos

Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Viral Mutations00:36

Viral Mutations

A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material for adaptive...
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Phylogenetic Trees03:21

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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The evolution of HIV: inferences using phylogenetics.

Eduardo Castro-Nallar1, Marcos Pérez-Losada, Gregory F Burton

  • 1Department of Biology, 401 Widtsoe Building, Brigham Young University, Provo, UT 84602-5181, USA. castronallar@gmail.com

Molecular Phylogenetics and Evolution
|December 6, 2011
PubMed
Summary

Molecular phylogenetics, especially coalescent theory, offers powerful tools for studying evolution. This review highlights advances in understanding Human Immunodeficiency Virus (HIV) evolution and dynamics using phylogenetic methods.

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Last Updated: May 27, 2026

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Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3

Published on: December 27, 2010

Area of Science:

  • Evolutionary biology
  • Genomics
  • Bioinformatics
  • Epidemiology
  • Ecology
  • Microbiology
  • Molecular biology
  • Biochemistry

Background:

  • Molecular phylogenetics has transformed evolutionary studies and related fields.
  • Coalescent theory has improved parameter estimation and hypothesis testing in population genetics.
  • Human Immunodeficiency Virus (HIV) is an ideal model for studying molecular evolution due to its characteristics.

Purpose of the Study:

  • To review significant advances in understanding HIV evolution using phylogenetic approaches.
  • To examine the roles of mutation and recombination in HIV molecular evolution and drug resistance.
  • To explore insights into HIV origin, diversification, and dynamics (phylodynamics).

Main Methods:

  • Application of phylogenetic approaches to study molecular evolution.
  • Analysis of mutation and recombination rates in HIV.
  • Utilizing coalescent theory for population genetics analyses.
  • Phylogenetic analysis for understanding HIV dynamics.

Main Results:

  • Phylogenetic methods have significantly advanced the study of HIV evolution.
  • Understanding of HIV's adaptive response to drug therapy and tissue tropism has improved.
  • Insights into HIV origin, diversification, and real-time molecular evolution have been gained.
  • Phylogenetic analysis has enhanced knowledge of HIV population dynamics (phylodynamics).

Conclusions:

  • Phylogenetic analysis is crucial for understanding HIV evolution, adaptation, and dynamics.
  • HIV serves as a valuable model for studying molecular evolution in real-time.
  • Continued application of phylogenetics will further elucidate complex viral evolutionary processes.