Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
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,...
Viral Structure00:56

Viral Structure

Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
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.
Phylogeny01:23

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Exploring epidemic control policies using nonlinear programming and mathematical models.

PLoS computational biology·2026
Same author

treestructure: an R package to detect population structure in phylogenetic trees.

Bioinformatics (Oxford, England)·2026
Same author

Complex dynamics between internalized HIV stigma, depression, and anxiety with panic among people with HIV.

AIDS (London, England)·2026
Same author

Robust phylodynamic inference and model specification for HIV transmission dynamics.

Epidemics·2025
Same author

Evidence for circulation of high-virulence HIV-1 subtype B variants in the United Kingdom.

Virus evolution·2025
Same author

Mitogenomes of mosquito species of Harris County in Texas.

Scientific reports·2025
Same journal

The microlandscapes of tree trunks: the effect of lichen and tree-level characteristics on arthropod communities.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same journal

Centimetre-scale landscapes to assess the motion behaviour and cognition of gastropods and bivalves.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same journal

Intertidal microcosms of wave-swept rocky shores: ecological and physiological insights from a uniquely stressful environment.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same journal

Temporal and spatial variation in temperature and oxygen at the microscale: key niche axes for aquatic life.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same journal

Natural microcosms in ecology: fulfilling the promise of model systems?

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
Same journal

Microbe-induced galls and plant defence: metabolite crosstalk in a co-evolutionary battle.

Philosophical transactions of the Royal Society of London. Series B, Biological sciences·2026
See all related articles

Related Experiment Video

Updated: May 14, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Modelling tree shape and structure in viral phylodynamics.

Simon D W Frost1, Erik M Volz

  • 1Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK. sdf22@cam.ac.uk

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
|February 6, 2013
PubMed
Summary
This summary is machine-generated.

Population structure significantly impacts viral phylogenies, affecting how sequences cluster. This study models HIV-1 transmission to reveal how structured populations influence evolutionary trees, even without strong selection.

More Related Videos

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
08:29

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

Modeling The Lifecycle Of Ebola Virus Under Biosafety Level 2 Conditions With Virus-like Particles Containing Tetracistronic Minigenomes
10:11

Modeling The Lifecycle Of Ebola Virus Under Biosafety Level 2 Conditions With Virus-like Particles Containing Tetracistronic Minigenomes

Published on: September 27, 2014

Related Experiment Videos

Last Updated: May 14, 2026

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
08:29

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Published on: October 21, 2014

Modeling The Lifecycle Of Ebola Virus Under Biosafety Level 2 Conditions With Virus-like Particles Containing Tetracistronic Minigenomes
10:11

Modeling The Lifecycle Of Ebola Virus Under Biosafety Level 2 Conditions With Virus-like Particles Containing Tetracistronic Minigenomes

Published on: September 27, 2014

Area of Science:

  • Epidemiology
  • Evolutionary Biology
  • Computational Biology

Background:

  • Population structure is crucial for understanding infectious disease transmission dynamics.
  • Human Immunodeficiency Virus type 1 (HIV-1) serves as a model system for studying viral evolution.
  • Phylogenetic tree shape can be influenced by population dynamics.

Purpose of the Study:

  • To investigate how population structure affects viral phylogeny shape and structure.
  • To analyze the impact of structured populations on phylogenetic trees in the absence of strong selection.
  • To develop methods for analyzing phylogenetic trees in structured populations.

Main Methods:

  • Development of deterministic approximations for phylogenetic tip dynamics.
  • Analysis of 'cherries' (tips sharing a common ancestor) as a measure of asymmetry and inter-group association.
  • Calculation of Sackin's index to quantify phylogenetic imbalance.
  • Modeling of heterogeneity in infectiousness and contact rates between groups.

Main Results:

  • The number of lineages over time is insufficient to describe phylogeny shape in structured populations.
  • Population structure may have minimal impact on overall tree asymmetry, particularly with small sample fractions.
  • Marked effects of population structure on the clustering and co-clustering of sequences from different subpopulations were observed.
  • Cherries serve as a dual measure for tree asymmetry and sequence association across groups.

Conclusions:

  • Population structure plays a significant role in shaping viral phylogenies, influencing sequence clustering.
  • Deterministic approximations provide insights into phylogenetic dynamics in structured populations.
  • Understanding population structure is key to interpreting viral evolutionary history, especially for diseases like HIV-1.