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

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...

Microbial Phylogeny

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,...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...

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?

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...

You might also read

Related Articles

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

Sort by

Same author

A phylogenomic framework of Gastrotricha evolutionary relationships.

Molecular phylogenetics and evolution·2026

Same author

From Rigid Order to Radical Variation: Mitogenome Evolution in the Main Lineages of a Lesser-Known Animal Phylum (Gastrotricha).

Genome biology and evolution·2026

Same author

SmithRNAs: A Common Feature among Metazoa.

Genome biology and evolution·2025

Same author

Convergent evolution in nuclear and mitochondrial OXPHOS subunits underlies the phylogenetic discordance in deep lineages of Squamata.

Molecular phylogenetics and evolution·2025

Same author

SmithHunter: a workflow for the identification of candidate smithRNAs and their targets.

BMC bioinformatics·2024

Same author

Mitochondrion-to-nucleus communication mediated by RNA export: a survey of potential mechanisms and players across eukaryotes.

Biology letters·2024

Search research articles

Related Experiment Video

Updated: Jun 13, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies.

Federico Plazzi¹, Ronald R Ferrucci, Marco Passamonti

¹Department of "Biologia Evoluzionistica Sperimentale", University of Bologna, Via Selmi 3, 40126 Bologna, Italy. federico.plazzi@unibo.it

BMC Bioinformatics

|April 29, 2010

Summary

This summary is machine-generated.

This study introduces a new method to evaluate phylogenetic representativeness using existing taxonomy. It helps researchers select optimal taxon samples for accurate evolutionary relationship reconstructions.

More Related Videos

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

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Related Experiment Videos

Last Updated: Jun 13, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

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

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Phylogenetics
Evolutionary Biology
Bioinformatics

Background:

Taxon sampling is critical for accurate phylogenetic analyses.
Incomplete or biased sampling can lead to erroneous evolutionary relationship reconstructions.
Existing methods often require prior knowledge of genetic relationships or established phylogenies, which are not always available.

Purpose of the Study:

To develop a novel method for assessing phylogenetic representativeness.
To provide a tool that relies solely on pre-existing taxonomic information.
To account for taxonomic instability and discordance.

Main Methods:

Utilized Clarke and Warwick statistics to measure phylogenetic representativeness.
Developed a Python-based script suite named PhyRe for analysis.
The method is based on the commonly known taxonomy of the ingroup.

Main Results:

The proposed method effectively discriminates between representative and unrepresentative taxon samples.
The method provides insights into adding taxa to enhance taxonomic coverage.
Phylogenetic representativeness serves as an objective criterion for planning phylogenetic studies.

Conclusions:

The developed method is sensitive and objective for evaluating taxon sampling strategies.
It aids in improving the reliability of phylogenetic studies.
Investigator expertise remains crucial, but this method offers an objective benchmark.