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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...

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.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...

The Tree of Life - Bacteria, Archaea, Eukaryotes

The Tree of Life - Bacteria, Archaea, Eukaryotes

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 extant and...

Evolutionary Relationships through Genome Comparisons

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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...

Phylogenetic Trees

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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...

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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: Jun 13, 2026

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Squirrel: Reconstructing Semi-directed Phylogenetic Level-1 Networks from Four-Leaved Networks or Sequence

Niels Holtgrefe¹, Katharina T Huber², Leo van Iersel¹

¹Delft Institute of Applied Mathematics, Delft University of Technology, Mekelweg 4, Delft 2628 CD, The Netherlands.

Molecular Biology and Evolution

|March 28, 2025

Summary

Biologists can now reconstruct complex evolutionary histories using phylogenetic networks, which better represent reticulate evolution than trees. The Squirrel algorithm efficiently builds these networks from sequence data, even for large datasets.

Keywords:

network reconstruction quarnet rooted phylogenetic network semi-directed phylogenetic network sequence alignment traveling salesman problem

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Genomic data availability is increasing, driving the need for sophisticated models of evolution.
Phylogenetic trees struggle to represent evolutionary histories involving secondary contact and reticulate evolution.
Semi-directed phylogenetic networks offer a more accurate representation of reticulate evolutionary events.

Purpose of the Study:

To introduce an algorithm for constructing semi-directed phylogenetic networks.
To develop a method for inferring these networks directly from sequence alignments.
To provide a computationally efficient tool for phylogenetic network reconstruction.

Main Methods:

Developed the Squirrel algorithm (Semi-directed Quarnet-based Inference to Reconstruct Level-1 Networks).
Implemented a heuristic for generating quarnets (four-leaf networks) from sequence alignments.
Tested the algorithm on simulated and real sequence datasets, including large alignments.

Main Results:

Squirrel successfully reconstructs semi-directed level-1 phylogenetic networks.
The algorithm is computationally efficient, producing results on a standard laptop within minutes.
Combinatorial consistency was proven for reconstructing triangle-free networks.

Conclusions:

Squirrel provides an efficient and accurate method for inferring phylogenetic networks from sequence data.
The tool facilitates the study of complex evolutionary histories involving reticulate events.
The Python implementation with a GUI is readily accessible for the research community.