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...

Microbial Phylogeny

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,...

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...

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...

Gene Duplication and Divergence

Gene Duplication and Divergence

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 characterized.

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.

You might also read

Related Articles

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

Sort by

Same author

LINC01234 Coordinates Protein Interactions and ceRNA Networks to Enhance YWHAZ-Driven Malignancy in Triple-Negative Breast Cancer.

Clinical breast cancer·2026

Same author

A straightforward access to specific bisindole systems related to caulersin.

Organic & biomolecular chemistry·2026

Same author

Postoperative anlotinib plus radiotherapy in patients with newly diagnosed, unmethylated O<sup>6</sup>-methylguanine-DNA methyltransferase glioblastoma: A single-arm, phase 2 study.

Cancer·2026

Same author

A Multi-Scale Edge-Preserving Decomposition and Fusion Framework for Multi-Polarization Passive Millimeter-Wave Imaging.

Sensors (Basel, Switzerland)·2026

Same author

Assessing climate-driven treeline dynamics via the habitat suitability index.

Journal of environmental management·2026

Same author

Chikusetsu saponin IVa mitigates septic cardiac injury by targeting DRP1 to suppress mitochondrial damage and NLRP3 inflammasome activation.

Life sciences·2026

Search research articles

Related Experiment Video

Updated: May 24, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A mixture framework for inferring ancestral gene orders.

Yiwei Zhang¹, Fei Hu, Jijun Tang

¹Center for Computational Biology, Beijing Forestry University, Beijing 100083, China. jtang@cse.sc.edu

|February 29, 2012

Summary

This summary is machine-generated.

A new mixture method accurately infers ancestral gene orders by combining maximum likelihood and parsimony approaches. This approach is faster and more accurate than existing methods, especially for genomes with high rearrangement rates.

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: May 24, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Inferring ancestral gene orders aids in understanding species evolution.
Current methods like GRAPPA and MGR (parsimony-based) are accurate but slow, especially at high rearrangement rates.
Maximum likelihood methods are faster but less accurate.

Purpose of the Study:

To develop a novel method for inferring ancestral gene orders that balances accuracy and computational efficiency.
To improve the analysis of evolutionary relationships between species.

Main Methods:

A hybrid approach combining maximum likelihood and parsimony-based direct optimization.
Utilizes maximum likelihood to identify probable ancestral gene adjacencies.
Fixes these adjacencies in a branch-and-bound search for median calculations.

Main Results:

The proposed mixture method significantly accelerates direct optimization techniques.
Maintains high accuracy even for distantly related genomes.
Outperforms maximum likelihood methods in accuracy.

Conclusions:

The mixture method offers superior accuracy and reduced computation time compared to existing parsimony and maximum likelihood methods.
Effectively handles genome data with high rearrangement rates, expanding analytical capabilities.
Provides a more robust tool for reconstructing ancestral genomes.