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

6.0K
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...
6.0K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.3K
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...
7.3K
Phylogenetic Trees03:21

Phylogenetic Trees

45.8K
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.
45.8K
Phylogeny01:23

Phylogeny

45.0K
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.
45.0K
The Fossil Record02:56

The Fossil Record

25.3K
The fossil record documents only a small fraction of all organisms that have ever inhabited Earth. Fossilization is a rare process, and most organisms never become fossils. Moreover, the fossil record only exhibits fossils that have been discovered. Nevertheless, sedimentary rock fossils of long-lived, abundant, hard-bodied organisms dominate the fossil record. These fossils offer valuable information, such as an organism's physical form, behavior, and age. Studying the fossil record helps...
25.3K
Synteny and Evolution02:31

Synteny and Evolution

3.3K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.3K

You might also read

Related Articles

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

Sort by
Same author

Assessing the Earliest Evidence for Life in the Geologic and Genomic Records.

Astrobiology·2026
Same author

Airway Malacia: Stent Innovations and Emerging Ex Vivo Testing Platforms.

Seminars in thoracic and cardiovascular surgery. Pediatric cardiac surgery annual·2026
Same author

Universal paralogs provide a window into evolution before the last universal common ancestor.

Cell genomics·2026
Same author

Horizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution.

Biology direct·2025
Same author

DupLoss-2: Improved Phylogenomic Species Tree Inference under Gene Duplication and Loss.

Systematic biology·2025
Same author

Enhancing the degradation of polystyrene and polyethylene terephthalate microplastics in water using electrochemical treatment at neutral pH.

Journal of environmental management·2025
Same journal

Cross-Domain Transfer Learning from Peptides to Metabolites Using a Multi-Property Fine-Tuned LLM.

Bioinformatics (Oxford, England)·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 11, 2025

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

DaTeR: error-correcting phylogenetic chronograms using relative time constraints.

Abhijit Mondal1, L Thiberio Rangel2, Jack G Payette2

  • 1Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA.

Bioinformatics (Oxford, England)
|February 8, 2023
PubMed
Summary
This summary is machine-generated.

Phylogenetic dating methods can now incorporate relative time constraints using the new DaTeR approach. This method improves chronogram accuracy by integrating both absolute and relative time data for evolutionary analysis.

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

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

Published on: July 11, 2025

161

Related Experiment Videos

Last Updated: Aug 11, 2025

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
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.4K
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

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

Published on: July 11, 2025

161

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic trees are dated using absolute time constraints from fossils.
  • Traditional methods struggle to incorporate relative time constraints, such as those from horizontal gene transfer.
  • This limitation can lead to inconsistencies between computed chronograms and known evolutionary events.

Purpose of the Study:

  • To introduce a novel phylogenetic dating approach, Dating Trees using Relative constraints (DaTeR).
  • To develop a method that integrates both absolute and relative time constraints for more accurate chronogram construction.
  • To address the inconsistencies arising from solely using absolute time constraints in phylogenetic dating.

Main Methods:

  • DaTeR utilizes Bayesian approaches to sample posterior chronograms based on absolute time constraints.
  • A constrained optimization framework is employed to minimally adjust sampled chronograms, satisfying relative time constraints.
  • The method aggregates results from multiple error-corrected chronograms for robust dating.

Main Results:

  • DaTeR was successfully applied to a dataset of 170 Cyanobacterial taxa with 24 relative constraints.
  • The approach demonstrated high effectiveness and scalability across six different molecular dating models.
  • Integration of relative constraints significantly improved the accuracy of estimated chronograms.

Conclusions:

  • DaTeR provides a robust and scalable solution for phylogenetic dating incorporating both absolute and relative time constraints.
  • The method enhances the accuracy and reliability of evolutionary timescale estimations.
  • DaTeR represents a significant advancement in computational phylogenetics.