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Phylogeny

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.

Phylogenetic Trees

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.

Evolutionary Relationships through Genome Comparisons

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...

Gene Evolution - Fast or Slow?

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...

Gene Evolution - Fast or Slow?

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Related Experiment Video

Updated: Nov 23, 2025

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

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

Published on: October 16, 2018

HIV Care Prioritization Using Phylogenetic Branch Length.

Niema Moshiri¹, Davey M Smith², Siavash Mirarab³

¹Departments of Computer Science and Engineering.

Journal of Acquired Immune Deficiency Syndromes (1999)

|January 4, 2021

Summary

Identifying individuals at high risk of transmitting HIV is crucial for public health resource allocation. A new phylogenetic method, Prioritization using AnCesTral edge lengths (ProACT), effectively prioritizes individuals for intervention, outperforming existing cluster-growth monitoring techniques.

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Last Updated: Nov 23, 2025

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

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Published on: October 16, 2018

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Prediction of HIV-1 Coreceptor Usage Tropism by Sequence Analysis using a Genotypic Approach

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Published on: December 1, 2011

Area of Science:

Molecular epidemiology
Phylogenetics
Public health

Background:

HIV transmission networks are often driven by a small number of individuals.
Public health interventions like antiretroviral therapy adherence are vital but resource-intensive.
Targeting high-risk individuals can optimize limited public health resources for HIV control.

Purpose of the Study:

To introduce Prioritization using AnCesTral edge lengths (ProACT), a novel phylogenetic approach.
To enhance the prioritization of individuals living with HIV for targeted interventions.
To improve the efficiency of public health resource allocation in HIV prevention.

Main Methods:

ProACT utilizes phylogenetic analysis of viral sequences.
Individuals are prioritized based on terminal and ancestral branch lengths in the phylogeny.
The method was evaluated on real-world HIV-1 subtype B data and simulation data.

Main Results:

ProACT demonstrated superior prioritization efficacy compared to monitoring cluster growth.
The method showed improved performance across various simulation and real-data sampling conditions.
ProACT effectively predicts individuals most likely to transmit HIV.

Conclusions:

ProACT offers a more effective prioritization strategy than current cluster-based methods.
The simple yet powerful approach of ProACT enhances the effectiveness of HIV intervention prioritization.
This method can significantly improve the targeting of limited public health resources to control HIV spread.