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...

Synteny and Evolution

Synteny and Evolution

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...

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?

You might also read

Related Articles

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

Sort by

Same author

Statistical and Structural Bias in Birth-Death Models.

Bulletin of mathematical biology·2026

Same author

The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis.

Nature communications·2024

Same author

Noise leads to the perceived increase in evolutionary rates over short time scales.

PLoS computational biology·2024

Same author

Author Correction: Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.

Nature communications·2024

Same author

Shifts in evolutionary lability underlie independent gains and losses of root-nodule symbiosis in a single clade of plants.

Nature communications·2024

Same author

A Novel Phylogenetic Negative Binomial Regression Model for Count-Dependent Variables.

Biology·2023

Search research articles

Related Experiment Video

Updated: Dec 27, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

On the Matrix Condition of Phylogenetic Tree.

Dwueng-Chwuan Jhwueng¹, Brian C O'Meara²

¹Department of Statistics, Feng Chia University, Taichung, Taiwan R.O.C.

Evolutionary Bioinformatics Online

|February 29, 2020

Summary

Phylogenetic comparative analyses can face instability issues when the phylogenetic covariance matrix becomes ill-conditioned. This study investigates this problem and proposes methods to improve the stability of evolutionary and ecological analyses.

Keywords:

Brownian motion condition number covariance matrix inversion phylogenetic comparative analysis phylogenetic tree

More Related Videos

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

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

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

Published on: July 11, 2025

Related Experiment Videos

Last Updated: Dec 27, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

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

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

Published on: July 11, 2025

Area of Science:

Evolutionary biology
Ecology
Phylogenetics
Comparative methods

Background:

Phylogenetic comparative analyses utilize evolutionary trees to study species' evolution and ecology.
A phylogenetic tree transforms into a phylogenetic covariance matrix, crucial for comparative methods.
Matrix inversion for likelihood calculations can be unstable if the matrix is ill-conditioned.

Purpose of the Study:

To investigate potential numerical instability in phylogenetic comparative analyses.
To identify issues arising from ill-conditioned phylogenetic covariance matrices.
To propose and evaluate methods for remedying matrix ill-conditioning.

Main Methods:

Algebraic transformation of phylogenetic trees into covariance matrices.
Analysis of matrix conditioning using eigenvalue ratios.
Development and testing of numerical stability improvement techniques.

Main Results:

Ill-conditioned phylogenetic covariance matrices can lead to unstable likelihood calculations and parameter estimates.
The ratio of maximum to minimum eigenvalues quantifies matrix ill-conditioning.
Proposed methods aim to enhance the stability of comparative analyses.

Conclusions:

Numerical stability is a critical consideration in phylogenetic comparative analyses.
Addressing ill-conditioned covariance matrices is essential for reliable evolutionary and ecological inferences.
Further research into robust computational methods is warranted.