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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...

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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.
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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: Jul 16, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Incomplete taxon sampling is not a problem for phylogenetic inference.

M S Rosenberg¹, S Kumar

¹Department of Biology, Arizona State University, Tempe, AZ 85287-1501, USA.

Proceedings of the National Academy of Sciences of the United States of America

|August 30, 2001

Summary

Phylogenetic inference accuracy is not improved by extensive taxon sampling. Longer DNA sequences, not more species, are key to reducing phylogenetic error and improving evolutionary history reconstruction.

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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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Area of Science:

Evolutionary Biology
Bioinformatics
Computational Biology

Background:

Taxon sampling is crucial for molecular phylogenetics, but insufficient sampling is a common error source.
Large datasets are often recommended to improve phylogenetic accuracy.
The impact of taxon sampling on phylogenetic inference requires further investigation.

Purpose of the Study:

To evaluate the effect of taxon sampling on phylogenetic inference accuracy.
To compare phylogenetic error rates between subsampled and full taxon sets.
To determine optimal strategies for improving phylogenetic accuracy.

Main Methods:

Computer simulations using evolutionary parameters from genomic databases.
Analysis of phylogenetic error per internal branch across different methods.
Comparison of trees inferred from subsampled versus complete taxon sets.

Main Results:

Phylogenetic error per internal branch was similar for subsampled and full taxon sets.
Neighbor-joining, minimum evolution, parsimony, and likelihood methods showed similar error patterns.
Inferred trees, regardless of taxon sample size, were equidistant from the true tree.

Conclusions:

Extensive taxon sampling does not significantly reduce phylogenetic error.
Longer molecular sequences are more effective than increased taxon sampling for improving phylogenetic accuracy.
Current phylogenetic inference methods may benefit more from sequence data enhancement.