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Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes

Kamaludin Dingle, Fatme Ghaddar, Petr Šulc, Ard A. Louis
doi: https://doi.org/10.1101/2020.12.03.410605
Kamaludin Dingle
1Centre for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
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  • For correspondence: Dingle.K@gust.edu.kw ard.louis@physics.ox.ac.uk
Fatme Ghaddar
1Centre for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
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Petr Šulc
2School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
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Ard A. Louis
3Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, United Kingdom
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  • For correspondence: Dingle.K@gust.edu.kw ard.louis@physics.ox.ac.uk
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Abstract

The relative prominence of developmental bias versus natural selection is a long standing controversy in evolutionary biology. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. By using the RNAshapes method to define coarse-grained SS classes, we can directly measure the frequencies that non-coding RNA SS shapes appear in nature. Our main findings are, firstly, that only the most frequent structures appear in nature: The vast majority of possible structures in the morphospace have not yet been explored. Secondly, and perhaps more surprisingly, these frequencies are accurately predicted by the likelihood that structures appear upon uniform random sampling of sequences. The ultimate cause of these patterns is not natural selection, but rather strong phenotype bias in the RNA genotype-phenotype (GP) map, a type of developmental bias that tightly constrains evolutionary dynamics to only act within a reduced subset of structures which are easy to “find”.

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 03, 2020.
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Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes
Kamaludin Dingle, Fatme Ghaddar, Petr Šulc, Ard A. Louis
bioRxiv 2020.12.03.410605; doi: https://doi.org/10.1101/2020.12.03.410605
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Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes
Kamaludin Dingle, Fatme Ghaddar, Petr Šulc, Ard A. Louis
bioRxiv 2020.12.03.410605; doi: https://doi.org/10.1101/2020.12.03.410605

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