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Updated: Dec 15, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Intragenic Conflict in Phylogenomic Data Sets.

Stephen A Smith¹, Nathanael Walker-Hale², Joseph F Walker³

¹Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.

Molecular Biology and Evolution

|July 14, 2020

Summary

Intragenic conflict, or conflicting evolutionary histories within a single gene, is common in phylogenomic data. This study found conflict varies widely, with alignment errors being a key contributor, necessitating new analysis methods.

Keywords:

intragenic conflict phylogenomics recombination

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Last Updated: Dec 15, 2025

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Published on: August 14, 2018

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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

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Published on: December 7, 2021

Area of Science:

Evolutionary Biology
Genomics
Bioinformatics

Background:

Phylogenetic analyses typically assume a single evolutionary history per gene.
Intragenic conflict, arising from biological processes or errors, can challenge this assumption.
The prevalence and sources of intragenic conflict in empirical data are not well understood.

Purpose of the Study:

To investigate the extent of well-supported intragenic conflict in large phylogenomic data sets.
To identify potential sources of this conflict, such as alignment errors.
To advocate for the routine analysis of within-gene phylogenetic signal.

Main Methods:

Examination of multiple large phylogenomic data sets from diverse taxa.
Application of a rapid and straightforward method for detecting intragenic conflict.
Detailed analysis of four exemplar genes and simulation of data under various scenarios.

Main Results:

Intragenic conflict was found to be highly variable across data sets, ranging from 1% to over 92% of genes.
Alignment error was identified as a significant contributor to intragenic conflict.
Unexplained conflict suggests potential biological signal or other error sources.

Conclusions:

Intragenic conflict is a prevalent phenomenon in phylogenomic data.
Alignment quality is crucial, but other factors also contribute to conflict.
Analyzing within-gene phylogenetic signal should be integrated into standard data analysis pipelines and biological exploration.