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

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 Trees03:21

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...
Microbial Phylogeny01:28

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,...
Evolutionary Relationships through Genome Comparisons02:54

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...
Phylogeny01:23

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...
Survival Tree01:19

Survival Tree

Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
 Building a Survival Tree
Constructing a survival tree begins...

You might also read

Related Articles

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

Sort by
Same author

Durum Wheat cv. Svevo Reference Genome Rel.2.0: A Comprehensive Tool for Wheat Genomics.

Plant biotechnology journal·2026
Same author

Beyond Synteny: A Scalable Phylogenomics Method for Whole-Genome Duplication Detection.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same author

A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications.

Journal of computational biology : a journal of computational molecular cell biology·2025
Same author

Time to publish responsibly: DAFNEE, a database of academia-friendly journals in ecology and evolutionary biology.

Journal of evolutionary biology·2025
Same author

Link between the Birth-Death Process and the Kingman Coalescent-Applications to Phylogenetic Epidemiology.

Systematic biology·2025
Same author

Mating systems and recombination landscape strongly shape genetic diversity and selection in wheat relatives.

Evolution letters·2024

Related Experiment Video

Updated: Jun 29, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhySIC_IST: cleaning source trees to infer more informative supertrees.

Celine Scornavacca1, Vincent Berry, Vincent Lefort

  • 1Institut des Sciences de l'Evolution (ISEM, UMR 5554 CNRS), Université Montpellier II, Place E, Bataillon - CC 064 - 34095 Montpellier Cedex 5, France. scornava@lirmm.fr

BMC Bioinformatics
|October 7, 2008
PubMed
Summary

New supertree methods, PhySIC_IST and STC, create more informative phylogenetic trees by selectively excluding conflicting taxa. This approach enhances resolution and accuracy in evolutionary analyses.

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

Tree Core Analysis with X-ray Computed Tomography
06:56

Tree Core Analysis with X-ray Computed Tomography

Published on: September 22, 2023

Related Experiment Videos

Last Updated: Jun 29, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Tree Core Analysis with X-ray Computed Tomography
06:56

Tree Core Analysis with X-ray Computed Tomography

Published on: September 22, 2023

Area of Science:

  • Phylogenetics and Evolutionary Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Supertree methods combine multiple phylogenetic trees, but topological conflicts can lead to poorly resolved and uninformative results.
  • Existing liberal and veto supertree methods struggle with significant conflicts or low taxon overlap, yielding uninformative supertrees.

Purpose of the Study:

  • To develop novel supertree methodologies that produce more informative phylogenies despite topological conflicts in source trees.
  • To introduce the concept of non-plenary supertrees, which exclude taxa with highly conflicting positions to improve resolution.

Main Methods:

  • Introduced PhySIC_IST, a variant of the PhySIC veto method, designed to infer non-plenary supertrees.
  • Developed a statistical preprocessing step, Source Trees Correction (STC), to identify and remove conflicting parts of source trees.
  • Combined STC with PhySIC_IST to balance veto and liberal approaches, tuned by a single parameter, and used a modified Cladistic Information Content (CIC) criterion for informativeness.

Main Results:

  • Large-scale simulations showed that STC+PhySIC_IST infers significantly more informative supertrees than PhySIC, with low Type I error rates comparable to MRP.
  • Biological case studies on animals confirmed STC's effectiveness in detecting source tree anomalies and STC+PhySIC_IST's ability to generate well-resolved supertrees consistent with current systematics.

Conclusions:

  • The proposed PhySIC_IST and STC methodologies offer a valuable approach for inferring non-plenary supertrees and preprocessing source trees.
  • These methods demonstrate improved informativeness and resolution in supertree construction, addressing limitations of existing techniques.
  • An implementation of PhySIC_IST and STC is publicly available for use in phylogenetic analyses.