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Updated: Oct 24, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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An Efficient, Nonphylogenetic Method for Detecting Genes Sharing Evolutionary Signals in Phylogenomic Data Sets.

Luiz Thibério Rangel1, Shannon M Soucy2, João C Setubal3

  • 1Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

Genome Biology and Evolution
|August 14, 2021
PubMed
Summary

The Evolutionary Similarity Index (IES) assesses shared evolution between gene families by analyzing sequence distances, bypassing complex gene tree comparisons. This method proves accurate and robust, identifying evolutionary trends and horizontal gene transfer patterns in archaeal genomes.

Keywords:
Archaeabioinformaticsclusteringgene coevolutionphylogenomics

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Assessing gene family evolutionary compatibility is vital but computationally intensive.
  • Gene tree comparisons are prone to errors from phylogenetic reconstruction and model choice.
  • Existing methods struggle with uncertainty in gene tree topologies.

Purpose of the Study:

  • Introduce the Evolutionary Similarity Index (IES) for robust gene family evolution assessment.
  • Develop a method that circumvents gene tree topology comparisons.
  • Enable many-to-many pairing of gene family copies to identify shared evolutionary trends.

Main Methods:

  • Applied weighted orthogonal distance regression to pairwise sequence distance matrices.
  • Utilized non-overlapping pairs of gene copies for many-to-many comparisons.
  • Analyzed simulated and empirical genomic data sets, including 1,322 genes from 42 archaeal genomes.

Main Results:

  • IES demonstrates accuracy comparable to tree-based methods, with reduced susceptibility to noise.
  • Identified eight major clusters of gene families with compatible evolutionary trends in Archaea.
  • Discovered accessory gene clusters suggesting interphyla horizontal gene transfer.

Conclusions:

  • IES offers a reliable and computationally efficient alternative for assessing gene family evolutionary compatibility.
  • The method successfully identified conserved and accessory gene clusters with distinct evolutionary patterns.
  • IES facilitates the study of evolutionary relationships and horizontal gene transfer in microbial genomes.