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

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.

Phylogenetic Trees

Phylogenetic Trees

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...

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.

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...

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,...

You might also read

Related Articles

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

Sort by

Same author

From Small Parsimony to Horizontal Gene Transfer: Inferring Horizontal Transfer and Gene Loss for Single-Origin Characters.

Journal of computational biology : a journal of computational molecular cell biology·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

FullSynesth: Syntenic Reconciliation of a Set of Consistent Gene Trees.

Theory of computing systems·2026

Same author

An overview of computational methods for gene prediction in eukaryotes: strengths, limitations, and future directions.

Bioinformatics advances·2025

Same author

Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.

Journal of molecular evolution·2025

Same author

Finding maximum common contractions between phylogenetic networks.

Algorithms for molecular biology : AMB·2025

Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026

Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

Same journal

SimMapNet: a Bayesian framework for gene regulatory network inference using gene ontology similarities as external hint.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 1, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Reconstructing a SuperGeneTree minimizing reconciliation.

Manuel Lafond, Aïda Ouangraoua, Nadia El-Mabrouk

BMC Bioinformatics

|October 10, 2015

Summary

This summary is machine-generated.

Reconstructing gene family evolution requires inferring super gene trees. This study defines the supergenetree problem, aiming to reconcile gene trees with species trees, and proves its computational hardness.

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

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Related Experiment Videos

Last Updated: Apr 1, 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

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Area of Science:

Computational Biology
Phylogenetics
Evolutionary Genomics

Background:

Supertrees are crucial for inferring large phylogenetic trees from partial datasets.
Classical supertree methods focus on species tree reconstruction.
Reconstructing gene trees requires reconciliation with a known species tree.

Purpose of the Study:

Define and analyze the supergenetree problem: finding a supertree of gene trees that minimizes reconciliation distance with a species tree.
Extend classical supertree methods to the supergenetree problem.
Investigate the computational complexity of the supergenetree problem and its variants.

Main Methods:

Extension of exact supertree algorithms to the supergenetree problem.
Development of a greedy heuristic for minimizing duplication cost.
Complexity analysis using NP-hardness proofs for approximation and specific cases.

Main Results:

Exact methods for supertrees are extended to the supergenetree problem, though they are computationally expensive.
A greedy heuristic is proposed for minimizing duplications.
The supergenetree problem and its variants are shown to be NP-hard to approximate.

Conclusions:

The supergenetree problem presents significant computational challenges, even for approximation.
New theoretical foundations are established for supertree algorithms in gene tree reconstruction.
The findings open avenues for further algorithmic exploration in evolutionary biology.