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Updated: Sep 4, 2025

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical

Alex R Gunderson¹, Liam J Revell^2,3

¹Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, 70118.

Evolution; International Journal of Organic Evolution

|July 19, 2022

Summary

Genetic assimilation, reduced plasticity during adaptation, can be falsely detected due to statistical artifacts like regression to the mean. Careful experimental design and analysis are crucial for accurate macroevolutionary studies.

Keywords:

Acclimation evolution global change plasticity reaction norm

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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
Genetics
Ecology

Background:

Genetic assimilation, a reduction in phenotypic plasticity during adaptation to new environments, is significant for understanding evolution under global change.
Clear null expectations are vital for testing genetic assimilation, but statistical artifacts and neutral evolution mechanisms can complicate interpretations.

Purpose of the Study:

To investigate the influence of regression to the mean and neutral evolution on detecting genetic assimilation using macroevolutionary simulations.
To assess the impact of experimental design and correction methods on the validity of genetic assimilation findings.

Main Methods:

Macroevolutionary numerical simulations were employed, varying factors like plasticity evolution, evolutionary mechanisms, trait measurement error, and experimental design.
A modified reaction norm correction method was used to address phylogenetic nonindependence.

Main Results:

Regression to the mean frequently generates spurious support for genetic assimilation.
Appropriate experimental design and post hoc corrections can mitigate these spurious effects.
Neutral evolution, depending on plasticity expression mechanisms, can mimic genetic assimilation patterns without selection.

Conclusions:

Macroevolutionary studies of genetic assimilation require significant caution due to pervasive statistical artifacts and potential for neutral processes to yield similar patterns.
Reanalysis of existing data revealed reduced support for genetic assimilation after applying appropriate corrections, highlighting the need for rigorous methodologies.