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Updated: Aug 12, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Phasing Gene Copies into Polyploid Subgenomes Using a Bayesian Phylogenetic Approach.

William A Freyman¹, Carl J Rothfels²

¹23andMe Inc., Sunnyvale, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)

|January 31, 2023

Summary

This summary is machine-generated.

Homologizer accurately phases gene copies into polyploid subgenomes using a Bayesian phylogenetic framework. This method ensures correct evolutionary history inference and detects non-homeologous sequences, improving phylogenetic analyses.

Keywords:

Allopolyploidy Homeologs Hybridization Phasing Polyploid phylogenetics Reticulate evolution RevBayes

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Area of Science:

Genomics
Evolutionary Biology
Bioinformatics

Background:

Polyploids possess multiple gene copies from distinct subgenomes, each with unique evolutionary trajectories.
Incorrectly phasing gene copies across loci violates phylogenetic assumptions, leading to erroneous evolutionary inferences.
Accurate subgenome assignment is critical for robust phylogenetic analysis in polyploid organisms.

Purpose of the Study:

To introduce and describe the application of the 'homologizer' tool for phasing gene copies into polyploid subgenomes.
To provide a flexible Bayesian phylogenetic method for inferring the probabilities of gene copy phasing.
To demonstrate the utility of 'homologizer' for hypothesis testing, including the detection of non-homeologous sequences.

Main Methods:

Utilizes a Bayesian phylogenetic framework to infer posterior probabilities of gene copy phasing.
Provides guidance on input data preparation and considerations for 'homologizer' analyses.
Employs Bayesian model comparison for hypothesis testing and detection of hidden paralogs or allelic variation.

Main Results:

Successfully demonstrates the phasing of gene copies into polyploid subgenomes using a basic 'homologizer' example.
Illustrates the application of 'homologizer' as a tool for detecting non-homeologous sequences.
Provides methods for visualizing and interpreting the results of 'homologizer' analyses.

Conclusions:

'Homologizer' offers a robust solution for accurate gene copy phasing in polyploids.
The method enhances the reliability of phylogenetic inference by ensuring correct subgenome assignment.
'Homologizer' serves as a valuable tool for exploring complex evolutionary histories and identifying sequence anomalies in polyploid genomes.