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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.

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.

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,...

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 Species Concept in Microbiology

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The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...

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Updated: May 31, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Terraces in phylogenetic tree space.

Michael J Sanderson¹, Michelle M McMahon, Mike Steel

¹Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA. sanderm@email.arizona.edu

Science (New York, N.Y.)

|June 18, 2011

Summary

This summary is machine-generated.

Researchers discovered new structures in evolutionary tree reconstruction, revealing "terraces" of similar trees. These findings aid in resolving phylogenetic ambiguity and improving evolutionary analyses using sequence data.

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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

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The ITS2 Database

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Area of Science:

Computational Biology
Evolutionary Biology
Bioinformatics

Background:

Constructing species-rich phylogenies is crucial for understanding the tree of life.
Multilocus sequence data sets are often incomplete, posing challenges for accurate phylogenetic reconstruction.

Purpose of the Study:

To describe previously unknown structure in the solution landscape of tree reconstruction.
To develop methods for characterizing and ameliorating phylogenetic ambiguity within identified structures.

Main Methods:

Analysis of the solution landscape for tree reconstruction problems.
Development of algorithms for identifying maximum-agreement subtrees.
Methods for selecting minimal sets of new sequencing targets.

Main Results:

Discovery of 'terraces' of trees with identical quality, arranged on islands of phylogenetically similar trees.
Efficient characterization of phylogenetic ambiguity within terraces.
Algorithms for ameliorating ambiguity via maximum-agreement subtrees or targeted sequencing.

Conclusions:

Phylogenetic ambiguity can be understood and managed by navigating the identified solution landscape.
New algorithms can improve the accuracy and efficiency of phylogenetic tree reconstruction.
Future tree-finding algorithms must account for large terraces in tree space.