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

51.8K
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.
51.8K
Phylogenetic Trees03:21

Phylogenetic Trees

6.8K
6.8K
Microbial Phylogeny01:28

Microbial Phylogeny

63
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,...
63
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

7.2K
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...
7.2K
Phylogeny01:23

Phylogeny

64.5K
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.
64.5K
The Tree of Life - Bacteria, Archaea, Eukaryotes02:40

The Tree of Life - Bacteria, Archaea, Eukaryotes

41.7K
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...
41.7K

You might also read

Related Articles

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

Sort by
Same author

Kente: A Graph-based Pangenomic Approach for Horizontal Gene Transfer Detection in Microbiomes.

bioRxiv : the preprint server for biology·2026
Same author

IQ-TREE 3: phylogenomic inference software using complex evolutionary models.

Molecular biology and evolution·2026
Same author

Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.

Methods in molecular biology (Clifton, N.J.)·2026
Same author

Gene tree discordance.

Current biology : CB·2026
Same author

Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.

bioRxiv : the preprint server for biology·2026
Same author

Ancestry-specific performance of variant effect predictors in clinical variant classification.

bioRxiv : the preprint server for biology·2026
Same journal

Quantitative genetics of lifetime growth curves in a lizard.

Evolution; international journal of organic evolution·2026
Same journal

Accounting for recombination rate variation improves inference of barrier loci and reveals the role of both natural and sexual selection in an incipient bird radiation.

Evolution; international journal of organic evolution·2026
Same journal

Linking fluvial barriers and habitat specialization in the evolution of microendemism in riverine fishes.

Evolution; international journal of organic evolution·2026
Same journal

Mutation rate variation as the neutral byproduct of developmental and life history diversification.

Evolution; international journal of organic evolution·2026
Same journal

Superorganismal Anisogamy: A Comparative Test of an Extended Theory.

Evolution; international journal of organic evolution·2026
Same journal

The role of microbial resource mutualists in plant adaptation to abiotic environments.

Evolution; international journal of organic evolution·2026
See all related articles

Related Experiment Video

Updated: Mar 29, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.7K

Irrational exuberance for resolved species trees.

Matthew W Hahn1,2, Luay Nakhleh3,4

  • 1Department of Biology, Indiana University, Bloomington, Indiana, 47405. mwh@indiana.edu.

Evolution; International Journal of Organic Evolution
|December 8, 2015
PubMed
Summary
This summary is machine-generated.

Phylogenomics can infer species trees, but traits may not follow these trees due to gene tree discordance. This phenomenon, hemiplasy, can lead to errors in analyzing trait evolution.

Keywords:
Comparative methodsconvergenceincomplete lineage sortingintrogression

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.3K
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

752

Related Experiment Videos

Last Updated: Mar 29, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

16.7K
A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

36.3K
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

752

Area of Science:

  • Evolutionary Biology
  • Phylogenetics
  • Genomics

Background:

  • Phylogenomics accurately infers species trees despite gene tree discordance.
  • Species trees are used to study trait evolution, including evolutionary changes and frequency.

Purpose of the Study:

  • To highlight issues with mapping traits onto single species trees.
  • To introduce and explain the phenomenon of hemiplasy in character evolution.

Main Methods:

  • Discussing the implications of gene tree discordance for trait mapping.
  • Outlining diagnostic methods for hemiplasy.
  • Proposing approaches to address hemiplasy in character mapping.

Main Results:

  • Traits may follow gene tree topologies discordant with the species tree.
  • Standard character mapping methods can misinfer the number of trait evolutions due to hemiplasy.
  • Hemiplasy poses significant challenges for phylogenetic inference.

Conclusions:

  • Hemiplasy necessitates careful consideration of gene tree discordance in trait evolution studies.
  • New methods are needed to accurately map traits and infer evolutionary history.
  • The focus on resolved species trees may overlook crucial evolutionary processes.