Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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.

Survival Tree

Survival Tree

Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
Building a Survival Tree
Constructing a...

Epiphytes, Parasites, and Carnivores

Epiphytes, Parasites, and Carnivores

Plants often form mutualistic relationships with soil-dwelling fungi or bacteria to enhance their roots’ nutrient uptake ability. Root-colonizing fungi (e.g., mycorrhizae) increase a plant’s root surface area, which promotes nutrient absorption. While root-colonizing, nitrogen-fixing bacteria (e.g., rhizobia) convert atmospheric nitrogen (N2) into ammonia (NH3), making nitrogen available to plants for various biological functions. For example, nitrogen is essential for the...

The Bronchial Tree

The Bronchial Tree

The human bronchi and bronchial tree play a crucial role in the respiratory system, facilitating the exchange of oxygen and carbon dioxide. Let's delve into the intricate structure and functions of these respiratory components.
The trachea, commonly known as the windpipe, is a tube that connects the larynx (voice box) to the bronchi. At a point called the carina, it bifurcates into two primary bronchi. The right primary bronchus is wider, shorter, and more vertical than the left primary...

Circuit Terminology

Circuit Terminology

An electrical network is a system composed of interconnected elements, such as resistors, capacitors, inductors, and voltage or current sources. Unlike a circuit, an electrical network does not necessarily form a closed path. In other words, while all circuits can be considered networks due to their interconnected nature, not every network qualifies as a circuit.
A circuit, on the other hand, is also an interconnected system of electrical elements but must contain one or more closed paths.

You might also read

Related Articles

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

Sort by

Same author

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence Alignments.

Molecular biology and evolution·2025

Same author

The hybrid number of a ploidy profile.

Journal of mathematical biology·2022

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 7, 2026

Quantifying Corticolous Arthropods Using Sticky Traps

Quantifying Corticolous Arthropods Using Sticky Traps

Published on: January 19, 2020

Arboreal networks and their underlying trees.

K T Huber¹, D Overman²

¹UEA, Norwich, England. k.huber@uea.ac.uk.

Journal of Mathematical Biology

|March 5, 2026

Summary

Horizontal gene transfer (HGT) is crucial for bacterial evolution. This study introduces a novel method for constructing arboreal networks, enhancing phylogenetic analyses of HGT across diverse bacterial ecological niches.

Keywords:

Arboreal network Augmented tree Enhanced quartet tree system Horizontal gene transfer Multiple-rooted network Phylogenetic tree

More Related Videos

Investigation of Plant Interactions Across Common Mycorrhizal Networks Using Rotated Cores

Investigation of Plant Interactions Across Common Mycorrhizal Networks Using Rotated Cores

Published on: March 26, 2019

A Method for Quantifying Foliage-Dwelling Arthropods

A Method for Quantifying Foliage-Dwelling Arthropods

Published on: October 20, 2019

Related Experiment Videos

Last Updated: Mar 7, 2026

Quantifying Corticolous Arthropods Using Sticky Traps

Quantifying Corticolous Arthropods Using Sticky Traps

Published on: January 19, 2020

Investigation of Plant Interactions Across Common Mycorrhizal Networks Using Rotated Cores

Investigation of Plant Interactions Across Common Mycorrhizal Networks Using Rotated Cores

Published on: March 26, 2019

A Method for Quantifying Foliage-Dwelling Arthropods

A Method for Quantifying Foliage-Dwelling Arthropods

Published on: October 20, 2019

Area of Science:

Evolutionary Biology
Bioinformatics
Computational Biology

Background:

Horizontal gene transfer (HGT) significantly impacts bacterial evolution, but current methods struggle to account for transfers between different ecological niches.
Phylogenetic networks offer a framework to model complex evolutionary histories, including HGT.

Purpose of the Study:

To develop methods for constructing arboreal networks, a type of phylogenetic network.
To advance the understanding of HGT inference by addressing limitations in current phylogeny-based approaches.

Main Methods:

Studying the combinatorial structure of arboreal networks.
Investigating the underlying tree of an arboreal network.
Extending existing encoding methods (triplets, trinets, quarnets) to arboreal networks.

Main Results:

Provides a method for constructing arboreal networks.
Complements existing encoding techniques for phylogenetic networks.
Offers a foundation for improved HGT inference methods.

Conclusions:

Understanding arboreal network construction is key to advancing HGT inference.
This work provides combinatorial tools for analyzing complex bacterial evolution.
The developed methods can enhance the study of gene flow across ecological boundaries.