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...

Genetics of Speciation

Genetics of Speciation

Speciation is the evolutionary process resulting in the formation of new, distinct species—groups of reproductively isolated populations.

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...

Phylogeny

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 kingdom.

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.

Gene Flow

Gene Flow

Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.

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

Ancestral state reconstruction with discrete characters using deep learning.

bioRxiv : the preprint server for biology·2026

Same author

A Phylogenetic Model of Established and Enabled Biome Shifts.

Systematic biology·2026

Same author

Phylogenetic estimation of diversity-dependent biogeographic rates 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

Search research articles

Related Experiment Video

Updated: Jun 17, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.

Fábio K Mendes¹, Michael J Landis²

¹Department of Biology, Louisiana State University, Baton Rouge, LA, USA.

Systematic Biology

|August 8, 2024

Summary

This summary is machine-generated.

PhyloJunction is a new open-source Python library for evolutionary modeling. It simplifies simulating, summarizing, and visualizing data for phylogenetic diversification models.

Keywords:

Evolutionary modeling graphical model simulation

More Related Videos

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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

Published on: May 28, 2021

Related Experiment Videos

Last Updated: Jun 17, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

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

Published on: May 28, 2021

Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Developing and testing evolutionary models is complex.
Existing tools may lack flexibility for diverse model implementations.
Phylogenetic diversification models are crucial for understanding evolutionary processes.

Purpose of the Study:

Introduce PhyloJunction, a flexible computational framework for evolutionary modeling.
Provide a user-friendly platform for prototyping, testing, and characterizing models.
Enable easier implementation and analysis of phylogenetic diversification models.

Main Methods:

Developed PhyloJunction as an open-source Python library.
Implemented a flexible graphical modeling architecture and a dedicated model specification language.
Integrated command-line and graphical interfaces for data simulation, summarization, and visualization.

Main Results:

PhyloJunction facilitates the prototyping, testing, and characterization of evolutionary models.
The framework supports a general implementation of a popular family of phylogenetic diversification models.
User interfaces streamline the workflow from model design to data analysis.

Conclusions:

PhyloJunction offers a versatile platform for evolutionary model development.
The library's architecture allows for future expansion to include new models and statistical learning applications.
PhyloJunction can serve as a valuable tool for research and education in evolutionary biology.