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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.

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.

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...

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...

Microbial Phylogeny

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,...

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Updated: May 12, 2026

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Relaxed phylogenetics and dating with confidence.

Alexei J Drummond¹, Simon Y W Ho, Matthew J Phillips

¹Department of Zoology, University of Oxford, Oxford, United Kingdom.

|May 11, 2006

Summary

This study introduces a new "relaxed phylogenetics" method for more accurate evolutionary tree inference. It estimates divergence times and measures evolutionary rate variation, outperforming traditional models.

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Last Updated: May 12, 2026

The ITS2 Database

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Published on: March 12, 2012

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 6, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Evolutionary Biology
Computational Biology
Phylogenetics

Background:

Phylogenetic inference traditionally uses unrooted or strict molecular clock models, which are biologically unrealistic.
The evolutionary process exists on a continuum between these extremes, necessitating intermediate models.
Relaxed molecular clock models offer a more realistic approach to phylogenetic analysis.

Purpose of the Study:

Introduce a novel approach for relaxed phylogenetic analysis.
Estimate phylogenies and divergence times with uncertainty in evolutionary rates and calibration points.
Quantify and compare the 'clocklikeness' of different datasets.

Main Methods:

Developed a new computational approach for relaxed phylogenetic analysis.
Applied the method to estimate phylogenies and divergence times.
Assessed rate autocorrelation and positioned datasets on a clocklikeness continuum.

Main Results:

Found no significant rate autocorrelation in three large datasets, questioning the necessity of autocorrelated models.
Demonstrated the method's ability to measure and compare dataset clocklikeness.
Analyzed diverse datasets including bacterial, yeast, plant, metazoan, and primate alignments.

Conclusions:

The new relaxed phylogenetics method is more accurate and precise than the unrooted model.
This approach successfully infers an evolutionary timescale.
It provides a robust framework for analyzing evolutionary rates and divergence times.