Abstract
Whole-genome duplications (WGDs) are important in shaping the evolution of complex genomes, including rewiring of genome regulation. To address key questions about how WGDs impact the evolution of genome regulation, we need to understand the relative importance of selection versus drift and temporal evolutionary dynamics. One promising class of statistical models that can help address such questions are phylogenetic Ornstein-Uhlenbeck (OU) models.
Here we present a computational pipeline for the comparative phylogenetic analyses of genome regulation using an OU model. We have implemented this model in R and provide a step-by-step protocol for the use of this model, including example scripts and simulated test data. We provide the nonspecialist a brief overview of how this model works and how to perform tests for signatures of selection on genome regulation as well as power simulations to aid in experimental design and interpretation of results. We believe that these resources could help polyploidy research move forward in an era of rapidly increasing functional genomics data across the tree of life.
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Acknowledgements
The study was funded by the Norwegian Research Council through the projects The role of whole genome duplication in vertebrate adaptation (project number 274669) and Transposable elements as agents of genome evolution and adaptation following a recent whole genome duplication (project number 275310).
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Arzumanova, K., Rohlfs, R.V., Grønvold, L., Strand, M.A., Hvidsten, T.R., Sandve, S.R. (2023). Analyses of Genome Regulatory Evolution Following Whole-Genome Duplication Using the Phylogenetic EVE Model. In: Van de Peer, Y. (eds) Polyploidy. Methods in Molecular Biology, vol 2545. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2561-3_11
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DOI: https://doi.org/10.1007/978-1-0716-2561-3_11
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