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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.

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...

Phylogenetic Trees

Phylogenetic Trees

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.

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

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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Related Experiment Video

Updated: Apr 12, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.

Ilyas R Sadreyev¹, Fei Ji², Emiliano Cohen³

¹Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.

Nucleic Acids Research

|May 11, 2015

Summary

Analyzing sequence conservation patterns across species helps predict protein function and identify new pathway members. This method reveals functional associations and uncharacterized protein roles.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Area of Science:

Comparative genomics
Bioinformatics
Evolutionary biology

Background:

Proteins within the same biological pathways or complexes often exhibit similar sequence conservation patterns across different species.
Loss or divergence of these proteins can indicate a reduced requirement for their associated pathways or complexes in certain lineages.

Purpose of the Study:

To predict functional associations between proteins using sequence conservation patterns.
To identify novel members of biological pathways and uncharacterized proteins.
To discover potential disease genes through phylogenetic profiling.

Main Methods:

Utilized normalized phylogenetic profiling to analyze sequence conservation across a large set of eukaryotic genomes.
Developed the PhyloGene web server for querying and visualizing phylogenetic profiles of conserved proteins.
Allowed protein queries via name selection or sequence input, comparing conservation across 86 animal, fungal, plant, and protist genomes.

Main Results:

Demonstrated that similarity in phylogenetic profiles can predict functional associations.
Successfully identified potential new pathway members and disease genes.
Provided a user-friendly platform (PhyloGene) for exploring protein conservation patterns.

Conclusions:

Phylogenetic profiling is a powerful approach for inferring protein function and biological relationships.
The PhyloGene server facilitates the exploration of evolutionary conservation for functional genomics research.
This method aids in understanding protein evolution and identifying genes with significant biological roles.