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

Phylogenetic Trees03:21

Phylogenetic Trees

48.6K
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.
48.6K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.6K
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...
6.6K
Phylogeny01:23

Phylogeny

55.9K
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.
55.9K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.7K
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...
7.7K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

36.7K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
36.7K
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

303
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...
303

You might also read

Related Articles

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

Sort by
Same author

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

PLoS computational biology·2026
Same author

RNAprecis: Prediction of full-detail RNA conformation from the experimentally best-observed sparse parameters.

bioRxiv : the preprint server for biology·2025
Same author

Medical graphics to improve patient understanding and anxiety in elderly and cognitively impaired patients scheduled for transcatheter aortic valve implantation (TAVI).

Clinical research in cardiology : official journal of the German Cardiac Society·2023
Same author

Statistical analysis of ENDOR spectra.

Proceedings of the National Academy of Sciences of the United States of America·2021
Same author

Two-site jumps in dimethyl sulfone studied by one- and two-dimensional <sup>17</sup>O NMR spectroscopy.

Journal of magnetic resonance (San Diego, Calif. : 1997)·2018
Same author

Connecting structurally and dynamically detected signatures of supramolecular Debye liquids.

The Journal of chemical physics·2017

Related Experiment Video

Updated: Nov 17, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.7K

Information geometry for phylogenetic trees.

M K Garba1,2, T M W Nye1, J Lueg3

  • 1School of Mathematics, Statistics and Physics, Newcastle University, Newcastle upon Tyne, UK.

Journal of Mathematical Biology
|February 16, 2021
PubMed
Summary
This summary is machine-generated.

We introduce wald space, a novel geometric framework for phylogenetic trees. This space brings trees closer if they generate similar genetic data distributions, offering a biologically grounded alternative for statistical analysis.

Keywords:
Information geometryPhylogenetic treeTree space

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

16.2K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

31.5K

Related Experiment Videos

Last Updated: Nov 17, 2025

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

35.7K
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.2K
The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

31.5K

Area of Science:

  • Computational Biology
  • Phylogenetics
  • Statistical Genetics

Background:

  • Existing phylogenetic tree spaces like BHV lack biologically principled geometries.
  • Current methods struggle with statistical analysis of phylogenies due to geometric limitations.

Purpose of the Study:

  • Introduce wald space, a new geometric space for phylogenetic trees.
  • Develop geometries based on biologically relevant assumptions for statistical analysis.
  • Compare wald space geometry with existing models like BHV.

Main Methods:

  • Defined wald space containing the BHV space and disconnected forests.
  • Investigated two geometries: Fisher information metric (discrete) and trace metric (continuous).
  • Developed gradient descent and geodesic computation algorithms.

Main Results:

  • Wald space offers a biologically motivated geometry where tree proximity reflects genetic data similarity.
  • Both discrete and continuous geometries in wald space are computationally tractable and similar.
  • Wald space geometry differs significantly from the BHV geometry.

Conclusions:

  • Wald space provides a novel and biologically principled framework for phylogenetic statistical analysis.
  • The developed geometries and computational methods enable practical application.
  • Wald space represents a significant advancement over existing phylogenetic tree spaces.