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

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.4K
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...
6.4K
Phylogenetic Trees03:21

Phylogenetic Trees

48.1K
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.
48.1K
Phylogeny01:23

Phylogeny

54.2K
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.
54.2K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

242
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...
242
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.5K
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...
7.5K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

177
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
177

You might also read

Related Articles

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

Sort by
Same author

Searching for Phylogenetic Networks.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

The phylogenetic relationships of Bokermann´s treefrogs: species groups, reproductive biology, and biogeography (Anura: Hylidae: Bokermannohyla).

Cladistics : the international journal of the Willi Hennig Society·2025
Same author

The limits of phylogenetic analysis: identifying analytical hallucinations.

Cladistics : the international journal of the Willi Hennig Society·2025
Same author

Phylogenetic minimum description length: an optimality criterion based on algorithmic complexity.

Cladistics : the international journal of the Willi Hennig Society·2025
Same author

Multi-armed bandits, Thomson sampling and unsupervised machine learning in phylogenetic graph search.

Cladistics : the international journal of the Willi Hennig Society·2024
Same author

PhylogeneticGraph (PhyG) a new phylogenetic graph search and optimization program.

Cladistics : the international journal of the Willi Hennig Society·2023
Same journal

Phylogenomics and the evolutionary history of the Oxyurida (pinworms).

Cladistics : the international journal of the Willi Hennig Society·2026
Same journal

Budding speciation, mitochondrial capture and introgression between surface and cave lineages in the Asellus aquaticus species complex.

Cladistics : the international journal of the Willi Hennig Society·2026
Same journal

Some considerations about Cotton and Wilkinson's "majority rule supertrees".

Cladistics : the international journal of the Willi Hennig Society·2026
Same journal

Phylogenomics and historical biogeography of the cosmopolitan velvet ant tribe Trogaspidiini (Hymenoptera: Mutillidae).

Cladistics : the international journal of the Willi Hennig Society·2026
Same journal

Monotypic genera: uninformative, but sometimes necessary.

Cladistics : the international journal of the Willi Hennig Society·2026
Same journal

Morphology-based phylogeny of longhorn beetles (Coleoptera, Cerambycidae) aligns with phylogenomics and informs higher-level systematics.

Cladistics : the international journal of the Willi Hennig Society·2026
See all related articles

Related Experiment Video

Updated: Oct 9, 2025

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

NUCLEIC ACID SEQUENCE PHYLOGENY AND RANDOM OUTGROUPS.

Ward C Wheeler1

  • 1Department of Invertebrates, American Museum of Natural History, Central Park West at 79th St., New York, NY 10024-5192, U.S.A.

Cladistics : the International Journal of the Willi Hennig Society
|December 22, 2021
PubMed
Summary
This summary is machine-generated.

Phylogenetic rooting using divergent taxa can be unreliable with nucleic acid sequences due to random similarity. This study proposes a test for outgroup reliability and an alternative rooting method using transformation matrices for accurate evolutionary analysis.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

9.9K

Related Experiment Videos

Last Updated: Oct 9, 2025

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 Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.5K
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
07:09

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

9.9K

Area of Science:

  • Evolutionary biology
  • Molecular evolution
  • Phylogenetics

Background:

  • Rooting phylogenetic networks with divergent taxa assumes shared historical character states.
  • Nucleic acid sequence data may exhibit random similarity in divergent outgroups, compromising historical inference.
  • Accurate rooting is crucial for understanding evolutionary relationships.

Purpose of the Study:

  • To propose a method for testing the reliability of divergent outgroups in phylogenetic rooting.
  • To introduce an alternative rooting procedure using asymmetrical character transformation matrices when suitable outgroups are unavailable.
  • To demonstrate these methods using alcohol dehydrogenase (ADH) gene sequences from Drosophila.

Main Methods:

  • Development of a procedure to statistically assess the historical similarity of outgroup characters.
  • Utilizing asymmetrical character transformation matrices to infer root position in the absence of a reliable outgroup.
  • Application and validation of the proposed methods on ADH sequence data within the Drosophila genus.

Main Results:

  • The proposed outgroup test can distinguish between historical similarity and random similarity in character states.
  • Asymmetrical transformation matrices can effectively provide polarity information for rooting phylogenetic networks.
  • The methods were successfully applied to Drosophila ADH sequences, yielding robust phylogenetic insights.

Conclusions:

  • Divergent outgroups require careful validation when rooting phylogenetic networks with molecular sequence data.
  • Character transformation matrices offer a viable alternative for phylogenetic rooting, especially when outgroup data is ambiguous.
  • These advancements improve the accuracy and reliability of phylogenetic reconstructions in molecular evolution studies.