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

Microbial Phylogeny01:28

Microbial Phylogeny

88
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,...
88
Phylogenetic Trees03:21

Phylogenetic Trees

41.6K
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.
41.6K
Phylogenetic Trees03:21

Phylogenetic Trees

5.7K
5.7K
Phylogeny01:23

Phylogeny

47.2K
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.
47.2K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.8K
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...
5.8K
Model Approaches for Pharmacokinetic Data: Distributed Parameter Models01:06

Model Approaches for Pharmacokinetic Data: Distributed Parameter Models

333
Pharmacokinetic models are mathematical constructs that represent and predict the time course of drug concentrations in the body, providing meaningful pharmacokinetic parameters. These models are categorized into compartment, physiological, and distributed parameter models.
The distributed parameter models are specifically designed to account for variations and differences in some drug classes. This model is particularly useful for assessing regional concentrations of anticancer or...
333

You might also read

Related Articles

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

Sort by
Same author

Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Summarizing Evolutionary Trajectories from Phylogenetic Character Maps of Discrete Traits.

bioRxiv : the preprint server for biology·2026
Same authorSame journal

An evolving view of phylogenetic biogeography.

Systematic biology·2026
Same author

How to date a molecular phylogeny: comparison of effective priors between node calibration and fossilized birth-death.

Proceedings. Biological sciences·2026
Same author

The nature and prevalence of diversification rate shifts across the Tree of Life.

Evolution letters·2026
Same author

Ancestral state reconstruction with discrete characters using deep learning.

bioRxiv : the preprint server for 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

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026
Same journal

Coalescent-based branch length estimation improves dating of species trees.

Systematic biology·2026
See all related articles

Related Experiment Video

Updated: Apr 27, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K

Probabilistic graphical model representation in phylogenetics.

Sebastian Höhna1, Tracy A Heath2, Bastien Boussau2

  • 1Department of Mathematics, Stockholm University, Stockholm, SE-106 91 Stockholm, Sweden; Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Bioinformatics and Evolutionary Genomics, Université de Lyon, Villeurbanne, France; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden; and Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia;Department of Mathematics, Stockholm University, Stockholm, SE-106 91 Stockholm, Sweden; Department of Evolution and Ecology, University of California, Davis, Storer Hall, One Shields Avenue, Davis, CA 95616, USA; Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA; Bioinformatics and Evolutionary Genomics, Université de Lyon, Villeurbanne, France; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden; and Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia; Sebastian.Hoehna@gmail.com.

Systematic Biology
|June 22, 2014
PubMed
Summary
This summary is machine-generated.

Graphical models offer a unified framework for statistical phylogenetics, simplifying complex models for better reproducibility and software development. This approach enhances understanding and accessibility for researchers.

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

14.3K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

6.8K

Related Experiment Videos

Last Updated: Apr 27, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.2K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

14.3K
Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

6.8K

Area of Science:

  • Statistical phylogenetics
  • Computational biology
  • Data science

Background:

  • The expanding model space in statistical phylogenetics necessitates improved methods for model representation and software development.
  • Clear model communication is vital for reproducibility, model evolution, and robust software design.
  • A unified framework simplifies complex phylogenetic models for a broader audience.

Purpose of the Study:

  • To introduce graphical models as a unifying framework for statistical phylogenetics.
  • To extend graphical model representations to phylogenetic analyses.
  • To develop novel components and modules for representing complex phylogenetic models.

Main Methods:

  • Application of graphical modeling principles to statistical phylogenetics.
  • Introduction of 'tree plates' for representing phylogenetic tree structures.
  • Development of modules for simplifying complex model components.

Main Results:

  • Demonstration of graphical models for representing diverse phylogenetic models.
  • Successful extension of graphical models to phylogenetics with 'tree plates'.
  • Facilitation of model representation for simulation and inference.

Conclusions:

  • Graphical models provide a comprehensible, flexible, and adaptable framework for phylogenetic modeling.
  • The proposed framework aids in teaching, communication, and the development of phylogenetic software.
  • Phylogenetic model graphs are applicable to simulation, maximum likelihood, and Bayesian inference.