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...

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...

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.

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.

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Applications of Molecular Taxonomy

Applications of Molecular Taxonomy

Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...

You might also read

Related Articles

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

Sort by

Same author

scDifformer: diffusion-based post-training for virtual cell modeling across large-scale single-cell data.

Nucleic acids research·2026

Same author

Capturing omega sign in the clinical assessment of depression by deep learning.

Translational psychiatry·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

TDLAS-based distributed monitoring method for multi-component gas leakage in crude oil storage tanks.

Optics express·2026

Same author

Global trends in robotic-assisted laparoscopic surgery (RALS): a bibliometric analysis (2000-2024).

Updates in surgery·2026

Same author

Activation of PPARγ and CPT1A Mediates the Hepatoprotective Effect of Ginsenoside CK against NAFLD in Rats.

Biological procedures online·2026

Search research articles

Related Experiment Video

Updated: Sep 13, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloTune: An efficient method to accelerate phylogenetic updates using a pretrained DNA language model.

Danruo Deng¹, Wuqin Xu², Bian Wu³

¹Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China.

Nature Communications

|July 27, 2025

Summary

PhyloTune accelerates phylogenetic tree construction by using a pretrained DNA language model to automatically identify informative DNA regions. This method efficiently integrates new species without manual marker selection.

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 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

Related Experiment Videos

Last Updated: Sep 13, 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 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

Area of Science:

Evolutionary Biology
Bioinformatics
Genomics

Background:

Phylogenetic tree construction is essential for understanding evolutionary history.
Increasing sequence data volume challenges traditional phylogenetic methods.
Integrating novel taxa into existing trees remains computationally intensive.

Purpose of the Study:

To develop a novel method for rapidly updating phylogenetic trees with new DNA sequences.
To leverage deep learning for automated identification of informative sequence regions.
To improve the efficiency and accuracy of phylogenetic analysis.

Main Methods:

Utilized a pretrained BERT network for DNA sequence representation learning.
Developed an approach to identify taxonomic units and relevant subtrees for updates.
Applied the PhyloTune method to simulated, plant (Embryophyta), and microbial (Bordetella) datasets.

Main Results:

PhyloTune effectively integrates novel taxa into existing phylogenetic trees.
The method automatically selects informative DNA regions, eliminating manual marker selection.
Demonstrated high performance on diverse simulated and empirical datasets.

Conclusions:

PhyloTune offers an efficient and automated solution for phylogenetic tree construction.
This approach facilitates deeper insights into evolutionary relationships and DNA sequence function.
The findings pave the way for enhanced understanding of genomic diversity and evolution.