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

7.2K
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...
7.2K
Microbial Phylogeny01:28

Microbial Phylogeny

22
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,...
22
Phylogenetic Trees03:21

Phylogenetic Trees

6.8K
6.8K
Phylogenetic Trees03:21

Phylogenetic Trees

51.7K
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.
51.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

8.4K
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...
8.4K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

3.8K
3.8K

You might also read

Related Articles

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

Sort by
Same author

Exploring life's hidden majority: microbial dark matter symposium highlights.

mSphere·2026
Same author

Applying Artificial Intelligence and machine learning in precision nutrition.

Nature communications·2026
Same author

Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper gastrointestinal tract.

Gut microbes·2026
Same author

Sparse regression, classification, and microbial network estimation in QIIME 2 with q2-classo and q2-gglasso.

ArXiv·2026
Same author

Identify contaminants with decontam on the QIIME 2 Framework.

Microbiology resource announcements·2026
Same author

A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.

bioRxiv : the preprint server for biology·2026

Related Experiment Video

Updated: Mar 25, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses.

Jennifer Fouquier1, Jai Ram Rideout2, Evan Bolyen3

  • 1Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA. jennietf@gmail.com.

Microbiome
|February 25, 2016
PubMed
Summary

Ghost-tree is a bioinformatics tool that combines two genetic markers to create accurate fungal phylogenetic trees for diversity analysis. This method improves the resolution of fungal community differences, enhancing our understanding of fungi in various environments.

More Related Videos

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

12.8K
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

740

Related Experiment Videos

Last Updated: Mar 25, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.6K
Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing
10:18

Amplification of Near Full-length HIV-1 Proviruses for Next-Generation Sequencing

Published on: October 16, 2018

12.8K
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

740

Area of Science:

  • Bioinformatics
  • Mycology
  • Computational Biology

Background:

  • Fungi are crucial in ecosystems but pose health and structural threats.
  • Next-generation sequencing of the internal transcribed spacer (ITS) region aids fungal diversity profiling.
  • High ITS sequence variability hinders accurate phylogenetic analysis across divergent fungi.

Purpose of the Study:

  • To develop a bioinformatics tool, ghost-tree, for constructing robust phylogenetic trees integrating multiple genetic markers.
  • To overcome limitations in aligning highly variable ITS sequences for phylogenetic analysis.
  • To enable more accurate fungal diversity analyses across evolutionarily distant taxa.

Main Methods:

  • Developed ghost-tree, a tool that integrates sequence data from two genetic markers into a single phylogenetic tree.
  • Constructed a "foundation" phylogeny using a conserved marker (e.g., 18S rRNA) for broad taxonomic coverage.
  • Built "extension" phylogenies using a variable marker (e.g., ITS) for closely related taxa and grafted them onto the foundation tree.

Main Results:

  • Applied ghost-tree to graft fungal ITS phylogenies onto an 18S rRNA foundation phylogeny.
  • Phylogenetic distances computed using ghost-tree explained significantly more variance in fungal community data compared to non-phylogenetic distances.
  • Ghost-tree metrics improved the ability to distinguish small differences between microbial communities.

Conclusions:

  • The Silva/UNITE-based ghost tree enhances resolution of fungal community differences in built environments.
  • Ghost-tree software can be integrated into existing fungal analysis pipelines.
  • The tool supports phylogenetic trees for other marker gene sets and bridges genome and amplicon trees.