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

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.

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.

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...

The Tree of Life - Bacteria, Archaea, Eukaryotes

The Tree of Life - Bacteria, Archaea, Eukaryotes

The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...

Modern Molecular Taxonomy

Modern Molecular Taxonomy

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...

You might also read

Related Articles

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

Sort by

Same author

ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies.

Genome research·2025

Same author

<i>Shishania</i> is a chancelloriid and not a Cambrian mollusk.

Science (New York, N.Y.)·2025

Same author

ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies.

bioRxiv : the preprint server for biology·2025

Same author

Organ systems of a Cambrian euarthropod larva.

Nature·2024

Same author

Protomelission is an early dasyclad alga and not a Cambrian bryozoan.

Nature·2023

Same author

The Cambrian cirratuliform <i>Iotuba</i> denotes an early annelid radiation.

Proceedings. Biological sciences·2023

Same journal

A novel phylogenomics pipeline reveals extensive topological conflict in the evolution of the angiosperm order Cucurbitales.

Systematic biology·2026

Same journal

Diversification dynamics in the global radiation of gobies.

Systematic biology·2026

Same journal

Correction to: nQMaker: Estimating Time Nonreversible Amino Acid Substitution Models.

Systematic biology·2026

Same journal

Phylogenomic challenges in polyploid-rich lineages: Insights from paralog processing and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae).

Systematic biology·2026

Same journal

An evolving view of phylogenetic biogeography.

Systematic biology·2026

Same journal

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 8, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Robust Analysis of Phylogenetic Tree Space.

Martin R Smith¹

¹Department of Earth Sciences, Durham University, Durham, UK.

Systematic Biology

|December 28, 2021

Summary

This summary is machine-generated.

Mapping phylogenetic trees in "tree space" can be misleading. Information-theoretic and quartet distances best represent tree similarity, while others like Robinson-Foulds distort relationships. Always validate tree space projections.

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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

Published on: July 11, 2025

Related Experiment Videos

Last Updated: Oct 8, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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

Published on: July 11, 2025

Area of Science:

Phylogenetics and evolutionary biology
Computational biology and bioinformatics

Background:

Phylogenetic analyses generate numerous trees, necessitating methods to visualize their relationships.
Mapping trees in 'tree space' aids in understanding search strategies and data differences, but dimensional reduction can cause distortions.

Purpose of the Study:

To evaluate the accuracy of low-dimensional tree space mappings using stratigraphic congruence.
To assess the utility of different tree distance metrics for representing phylogenetic similarity.

Main Methods:

Analysis of 128 morphological data sets and their resulting phylogenetic trees.
Comparison of tree similarity using various distance metrics (information-theoretic, quartet, Robinson-Foulds, Kendall-Colijn).
Evaluation of low-dimensional projections (2D, 3D) against true distances and stratigraphic congruence.

Main Results:

Information-theoretic and quartet distances provide the most accurate representation of phylogenetic similarity in tree space.
Robinson-Foulds distances lead to significant distortions, and Kendall-Colijn distances are heavily influenced by tree shape.
Low-dimensional mappings (2D, 3D) often fail to capture true tree relationships and clustering structure.

Conclusions:

Tree space projections require explicit validation to ensure accurate representation of phylogenetic relationships.
The choice of distance metric critically impacts the interpretation of tree space visualizations.
Recommendations for validation and visualization are implemented in the 'TreeDist' R package.