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

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
Phylogenetic Trees03:21

Phylogenetic Trees

45.6K
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.
45.6K
Phylogeny01:23

Phylogeny

44.6K
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.
44.6K
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

6.2K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.2K
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

6.0K
Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
6.0K
Homologous Recombination02:31

Homologous Recombination

4.7K
4.7K

You might also read

Related Articles

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

Sort by
Same author

Development of a predictive model based on ultrasonographic features of brucella-associated periarthritis of the shoulder.

Frontiers in cellular and infection microbiology·2026
Same author

Ligilactobacillus salivarius Lbs57 Exerted Antibacterial Activity and Modulated Cecal Microbiota to Reduce Foodborne Pathogen Campylobacter jejuni.

Probiotics and antimicrobial proteins·2026
Same author

Targeting the JAK/STAT pathway with isoliquiritigenin in ovarian cancer: molecular mechanisms and therapeutic implications.

Frontiers in pharmacology·2026
Same author

Retraction notice to "Oxytocin with calcium vs. oxytocin for induction of labor in women with term premature rupture of membranes: A randomized controlled trial" [AM J Obstet Gynecol MFM 6 (2024) 101502].

American journal of obstetrics & gynecology MFM·2026
Same author

Efficacy analysis of early incision and drainage on necrotizing fasciitis, a retrospective study.

BMC infectious diseases·2026
Same author

Albumin-to-globulin ratio and neutrophil percentage as predictive markers for necrotizing fasciitis prognosis.

Burns : journal of the International Society for Burn Injuries·2026

Related Experiment Video

Updated: Jul 23, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K

Espalier: Efficient Tree Reconciliation and Ancestral Recombination Graphs Reconstruction Using Maximum Agreement

David A Rasmussen1,2, Fangfang Guo1

  • 1Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695, USA.

Systematic Biology
|July 17, 2023
PubMed
Summary

Reconstructing ancestral recombination graphs (ARGs) is challenging. This study introduces a novel method using maximum agreement forests (MAFs) to reconcile phylogenetic trees, improving ARG accuracy and efficiency for genomic data analysis.

Keywords:
Ancestral recombination graphmaximum agreement forestphylogenetic discordancerecombinationreconciliation

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

16.0K
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

12.2K

Related Experiment Videos

Last Updated: Jul 23, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.0K
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

12.2K

Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Genomics

Background:

  • Recombination creates mosaic genomes with varying ancestral histories.
  • Reconstructing ancestral recombination graphs (ARGs) from genomic data is computationally complex.

Purpose of the Study:

  • To develop a method for reconciling discordant phylogenetic trees to reconstruct ARGs.
  • To improve the accuracy and efficiency of ARG reconstruction.

Main Methods:

  • Utilized maximum agreement forests (MAFs) to identify concordant subtrees between discordant phylogenetic trees.
  • Developed a reconciliation approach to retain supported discordances and minimize phylogenetic noise.
  • Combined MAFs and reconciliation to select optimal local trees across the genome for ARG construction.

Main Results:

  • The heuristic ARG reconstruction method is computationally efficient and comparable in accuracy to exact methods.
  • Reconstructed ARGs accurately estimate demographic parameters like recombination rates.
  • Successfully applied the method to Potyvirus RNA viruses, distinguishing true recombination from noise.

Conclusions:

  • The MAF-based approach offers an efficient and accurate method for ARG reconstruction.
  • This method aids in understanding complex evolutionary histories shaped by recombination.
  • The approach is valuable for analyzing viral evolution and distinguishing biological signals from data artifacts.