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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.

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Phylogenetic Trees

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Modern Molecular Taxonomy

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The Tree of Life - Bacteria, Archaea, Eukaryotes

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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...

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Related Experiment Video

Updated: Nov 29, 2025

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

eMPRess: a systematic cophylogeny reconciliation tool.

Santi Santichaivekin¹, Qing Yang¹, Jingyi Liu¹

¹Department of Computer Science, Harvey Mudd College, Claremont, CA 91711, USA.

Bioinformatics (Oxford, England)

|November 20, 2020

Summary

This summary is machine-generated.

We introduce eMPRess, a new software for phylogenetic tree reconciliation. This tool helps researchers make stronger inferences using the duplication-transfer-loss model by improving event cost selection and solution representation.

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Last Updated: Nov 29, 2025

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

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 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:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Phylogenetic tree reconciliation is crucial for understanding evolutionary relationships.
The duplication-transfer-loss model is a standard framework for this analysis.
Choosing appropriate event costs and representative solutions remains a challenge.

Purpose of the Study:

To present eMPRess, a novel software program for phylogenetic tree reconciliation.
To address the challenges of selecting event costs and representative solutions within the duplication-transfer-loss model.
To enable more robust evolutionary inferences for researchers.

Main Methods:

Development of the eMPRess software.
Implementation of systematic approaches for choosing event costs.
Integration of methods for selecting representative reconciliation solutions.

Main Results:

eMPRess provides a systematic framework for phylogenetic tree reconciliation.
The software facilitates more robust inferences by addressing key methodological challenges.
Users can achieve more reliable evolutionary analyses with eMPRess.

Conclusions:

eMPRess offers a valuable tool for the bioinformatics community.
The software enhances the reliability of phylogenetic tree reconciliation.
eMPRess supports advanced evolutionary studies through improved computational methods.