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

View ORCID ProfileAlex R. Gunderson, View ORCID ProfileLiam J. Revell
doi: https://doi.org/10.1101/2021.12.28.473512
Alex R. Gunderson
1Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
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  • For correspondence: agunderson@tulane.edu
Liam J. Revell
2Department of Biology, University of Massachusetts Boston, Boston, MA, USA
3Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
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Abstract

Genetic assimilation is a process that leads to reduced phenotypic plasticity during adaptation to novel conditions, a potentially important phenomenon under global environmental change. Null expectations when testing for genetic assimilation, however, are not always clear. For instance, the statistical artifact of regression to the mean could bias us towards detecting genetic assimilation when it has not occurred. Likewise, the specific mechanism underlying plasticity expression may affect null expectations under neutral evolution. We used macroevolutionary numerical simulations to examine both of these important issues and their interaction, varying whether or not plasticity evolves, the evolutionary mechanism, trait measurement error, and experimental design. We also modified an existing reaction norm correction method to account for phylogenetic non-independence. We found: 1) regression to the mean is pervasive and can generate spurious support for genetic assimilation; 2) experimental design and post-hoc correction can minimize this spurious effect; and 3) neutral evolution can produce patterns consistent with genetic assimilation without constraint or selection, depending on the mechanism of plasticity expression. Additionally, we re-analyzed published macroevolutionary data supporting genetic assimilation, and found that support was lost after proper correction. Considerable caution is thus required whenever investigating genetic assimilation and reaction norm evolution at macroevolutionary scales.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 30, 2021.
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Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical considerations
Alex R. Gunderson, Liam J. Revell
bioRxiv 2021.12.28.473512; doi: https://doi.org/10.1101/2021.12.28.473512
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Testing for genetic assimilation with phylogenetic comparative analysis: Conceptual, methodological, and statistical considerations
Alex R. Gunderson, Liam J. Revell
bioRxiv 2021.12.28.473512; doi: https://doi.org/10.1101/2021.12.28.473512

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