ArticleJournal of the Royal Society, Interface2023
The non-deterministic genotype-phenotype map of RNA secondary structure.
Article in Journal of the Royal Society, Interface, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The adaptive landscapes of three globaleLife · 2026Article
- A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps.PLoS computational biology · 2026Article
- Evolutionary dynamics under phenotypic uncertainty.bioRxiv : the preprint server for biology · 2026Article
- Challenges and opportunities in technologies and methods for lncRNA structure determination.Cell & bioscience · 2025Review
- Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation.Molecular biology and evolution · 2024Article
- The Boltzmann distributions of molecular structures predict likely changes through random mutations.Biophysical journal · 2023Article
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Authors and funding
3 authors.
Funding
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Abstract
Selection and variation are both key aspects in the evolutionary process. Previous research on the mapping between molecular sequence (genotype) and molecular fold (phenotype) has shown the presence of several structural properties in different biological contexts, implying that these might be universal in evolutionary spaces. The deterministic genotype-phenotype (GP) map that links short RNA sequences to minimum free energy secondary structures has been studied extensively because of its computational tractability and biologically realistic nature. However, this mapping ignores the phenotypic plasticity of RNA. We define a GP map that incorporates non-deterministic (ND) phenotypes, and take RNA as a case study; we use the Boltzmann probability distribution of folded structures and examine the structural properties of ND GP maps for RNA sequences of length 12 and coarse-grained RNA structures of length 30 (RNAshapes30). A framework is presented to study robustness, evolvability and neutral spaces in the ND map. This framework is validated by demonstrating close correspondence between the ND quantities and sample averages of their deterministic counterparts. When using the ND framework we observe the same structural properties as in the deterministic GP map, such as bias, negative correlation between genotypic robustness and evolvability, and positive correlation between phenotypic robustness and evolvability.
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