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

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.

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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

Speciation Rates

Speciation Rates

You might also read

Related Articles

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

Sort by

Same author

GTRspmix: Capturing Heterogeneity of Exchangeabilities Across Sites to Improve Protein Phylogenetics.

bioRxiv : the preprint server for biology·2026

Same author

Modeling Site-and-Branch-Heterogeneity with GFmix.

Systematic biology·2026

Same author

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

Molecular biology and evolution·2026

Same author

Comparing partition and mixture models with akaike information criteria.

Systematic biology·2026

Same author

The LECA had a conventional kinetochore and the kinetoplastid kinetochore is a derived feature - a critical evaluation of Akiyoshi, 2025.

Journal of cell science·2026

Same author

Pangenome biology and evolution in harmful algal-bloom-forming pelagophytes.

Current biology : CB·2025

Search research articles

Related Experiment Video

Updated: Nov 19, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Long Branch Attraction Biases in Phylogenetics.

Edward Susko¹, Andrew J Roger²

¹Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada.

Systematic Biology

|February 2, 2021

Summary

Long branch attraction (LBA) in phylogenetics is often caused by differing model space sizes. This bias, especially with partitioned data, can be addressed using bootstrap bias corrections for accurate phylogenetic tree estimation.

More Related Videos

Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton

Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton

Published on: May 7, 2016

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Related Experiment Videos

Last Updated: Nov 19, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton

Dissection and Flat-mounting of the Threespine Stickleback Branchial Skeleton

Published on: May 7, 2016

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Area of Science:

Phylogenetics
Computational Biology
Evolutionary Biology

Background:

Long branch attraction (LBA) is a significant bias in phylogenetic inference.
The underlying causes of LBA are not fully understood.
LBA is particularly problematic when analyzing partitioned datasets.

Purpose of the Study:

To investigate the role of model space size in long branch attraction.
To propose methods for correcting LBA bias in phylogenetic estimation.
To enhance the accuracy of phylogenetic tree reconstruction.

Main Methods:

Formulating phylogenetic tree estimation as a model selection problem.
Utilizing maximum likelihood methods for phylogenetic analysis.
Applying bootstrap bias corrections to assess estimation accuracy.

Main Results:

Differences in effective model space sizes contribute significantly to LBA.
Trees with longer branches offer more flexibility in parameter estimation, increasing bias.
Bootstrap bias corrections serve as effective cross-checks for LBA.

Conclusions:

LBA is largely driven by variations in the flexibility of parameter estimation across different tree topologies.
Treating phylogenetic estimation as model selection highlights the impact of effective model space size.
Bootstrap bias corrections are a valuable tool for mitigating LBA in phylogenetics.