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

Microbial Phylogeny01:28

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,...
Phylogenetic Trees03:21

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Evolutionary Relationships through Genome Comparisons02:54

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...
Phylogeny01:23

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

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...

You might also read

Related Articles

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

Sort by
Same author

Fatigue reduction by sequential stimulation of multiple motor points in a muscle.

Clinical orthopaedics and related research·1995
Same author

Prospective, auto-controlled study on reinsemination of failed-fertilized oocytes by intracytoplasmic sperm injection.

Fertility and sterility·1995
Same author

Fluidity of the lipid domain of cell wall from Mycobacterium chelonae.

Proceedings of the National Academy of Sciences of the United States of America·1995
Same author

Effect of oleanolic acid on hepatic toxicant-activating and detoxifying systems in mice.

The Journal of pharmacology and experimental therapeutics·1995
Same author

Denaturant unfolding of the ferric enterobactin receptor and ligand-induced stabilization studied by site-directed spin labeling.

Biochemistry·1995
Same author

Identification of an essential cysteinyl residue in the ArsC arsenate reductase of plasmid R773.

Biochemistry·1995

Related Experiment Video

Updated: Jun 3, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Bayes estimators for phylogenetic reconstruction.

P M Huggins1, W Li, D Haws

  • 1Lane Center for Computational Biology, Carnegie Mellon University, Mellon Institute Building, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.

Systematic Biology
|April 8, 2011
PubMed
Summary
This summary is machine-generated.

We introduce a Bayesian approach to phylogenetic tree reconstruction, finding the "median" tree that is closest on average to sample trees. This Bayes estimator (BE) improves accuracy over methods like maximum likelihood (ML).

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

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Related Experiment Videos

Last Updated: Jun 3, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Phylogenetics
  • Computational Biology
  • Statistical Modeling

Background:

  • Phylogenetic tree reconstruction methods are typically evaluated by accuracy, but common approaches like maximum likelihood (ML) do not directly optimize for this.
  • Existing methods may not explicitly aim to minimize the distance between the reconstructed tree and the true evolutionary history.

Purpose of the Study:

  • To propose a novel Bayesian solution for phylogenetic tree reconstruction that directly maximizes accuracy.
  • To introduce the Bayes estimator (BE) as a "median" tree that is closest on average to a set of sampled trees.

Main Methods:

  • The study proposes finding the Bayes estimator (BE) by identifying the tree that minimizes the average distance to a collection of tree samples.
  • A unified framework for BE trees is discussed, with a focus on tree distances quantifiable as squared Euclidean distances, including Robinson-Foulds (RF) distance, quartet distance, and squared path difference.
  • Bayes estimators are practically estimated using a hill-climbing algorithm.

Main Results:

  • Simulations and real data analyses demonstrate that BEs can be effectively estimated using hill-climbing.
  • Bayes estimators (BEs) showed improved accuracy, being closer to the true tree compared to maximum likelihood (ML) and neighbor joining methods.
  • The BE optimized under squared path difference exhibited strong performance across both squared path difference and Robinson-Foulds (RF) distance metrics.

Conclusions:

  • The proposed Bayesian approach offers a more accurate method for phylogenetic tree reconstruction by directly optimizing for tree accuracy.
  • Bayes estimators provide a statistically grounded alternative to existing methods, particularly when accuracy is the primary evaluation criterion.
  • The BE, especially under squared path difference, shows promise for robust phylogenetic inference across different distance measures.