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

Phylogenetic Trees03:21

Phylogenetic Trees

48.3K
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.
48.3K
Phylogeny01:23

Phylogeny

55.1K
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.
55.1K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.5K
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...
6.5K
Protein Networks02:26

Protein Networks

4.2K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.2K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

298
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
298
Synteny and Evolution02:31

Synteny and Evolution

3.4K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.4K

You might also read

Related Articles

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

Sort by
Same author

Quantifying the difference between phylogenetic diversity and diversity indices.

Journal of mathematical biology·2024
Same author

Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks.

Journal of mathematical biology·2020
Same journal

Phenotypic plasticity trade-offs in an age-structured model of bacterial growth under stress.

Journal of mathematical biology·2026
Same journal

Intraspecific interactions facilitate mutualism across multilayer networks under weak selection.

Journal of mathematical biology·2026
Same journal

A two-species competition model on a compact metric graph for the invasion and competition of Aedes Aegypti and Aedes Albopictus mosquitoes in Florida.

Journal of mathematical biology·2026
Same journal

Superinfection and the hypnozoite reservoir for Plasmodium vivax: a multitype branching process approximation.

Journal of mathematical biology·2026
Same journal

Correction to: Superinfection and the hypnozoite reservoir for Plasmodium vivax: a general framework.

Journal of mathematical biology·2026
Same journal

Stoichiometric balance and sustained rhythms.

Journal of mathematical biology·2026
See all related articles

Related Experiment Video

Updated: Oct 23, 2025

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.5K

Trinets encode orchard phylogenetic networks.

Charles Semple1, Gerry Toft2

  • 1School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand. charles.semple@canterbury.ac.nz.

Journal of Mathematical Biology
|August 22, 2021
PubMed
Summary
This summary is machine-generated.

Trinets, a type of phylogenetic network, can fully represent rooted binary orchard networks. This study introduces a polynomial-time algorithm for constructing these networks from trinets, answering a key question in phylogenetics.

Keywords:
Level-k networksOrchard networksTree-child networksTrinets

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.1K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

327

Related Experiment Videos

Last Updated: Oct 23, 2025

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
09:49

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

Published on: September 25, 2021

4.5K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.1K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

327

Area of Science:

  • Computational phylogenetics
  • Graph theory
  • Bioinformatics

Background:

  • Rooted triples are sufficient to encode rooted binary phylogenetic trees.
  • This sufficiency does not generally hold for rooted binary phylogenetic networks.
  • Rooted binary orchard networks generalize rooted binary tree-child networks.

Purpose of the Study:

  • To demonstrate that trinets are sufficient to encode rooted binary orchard networks.
  • To develop a polynomial-time algorithm for constructing rooted binary orchard networks from trinets.
  • To address the question of polynomial-time construction for rooted binary tree-child networks.

Main Methods:

  • Utilizing trinets as fundamental units for representing phylogenetic networks.
  • Developing and analyzing a novel polynomial-time algorithm.
  • Generalizing concepts from rooted triples to trinets and from trees to networks.

Main Results:

  • Trinets are proven to be sufficient for encoding rooted binary orchard networks.
  • A polynomial-time algorithm for constructing rooted binary orchard networks from trinets is presented.
  • The algorithm provides an affirmative answer to the existence of a polynomial-time method for rooted binary tree-child networks.

Conclusions:

  • The study establishes the sufficiency of trinets for rooted binary orchard networks.
  • The developed algorithm offers an efficient method for network reconstruction.
  • This work advances computational methods in phylogenetic network analysis.