ArticleJournal of the Royal Society, Interface2015
The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.
Article in Journal of the Royal Society, Interface, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed.
- A simple model captures key characteristics of biological non-deterministic genotype-phenotype maps.PLoS computational biology · 2026Article
- Hierarchical genotype networks and incipient ecological speciation in Q[Formula: see text] phage quasispecies.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Predicting the topography of fitness landscapes from the structure of genotype-phenotype maps.Genetics · 2026Article
- Bounding phenotype transition probabilities via conditional complexity.Journal of the Royal Society, Interface · 2025Article
- Article
- Bias in the arrival of variation can dominate over natural selection in Richard Dawkins's biomorphs.PLoS computational biology · 2024Article
- The non-deterministic genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2023Article
- Maximum mutational robustness in genotype-phenotype maps follows a self-similar blancmange-like curve.Journal of the Royal Society, Interface · 2023Article
- Genotype-phenotype mapping with polyominos made from DNA origami tiles.Biophysical journal · 2022Article
- The structure of genotype-phenotype maps makes fitness landscapes navigable.Nature ecology & evolution · 2022Article
- Fast free-energy-based neutral set size estimates for the RNA genotype-phenotype map.Journal of the Royal Society, Interface · 2022Article
- Gene duplication and subsequent diversification strongly affect phenotypic evolvability and robustness.Royal Society open science · 2021Article
- On the evolution and development of morphological complexity: A view from gene regulatory networks.PLoS computational biology · 2021Article
- Using small samples to estimate neutral component size and robustness in the genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2020Article
- On the emergence of structural complexity in RNA replicators.RNA (New York, N.Y.) · 2019Article
- Model genotype-phenotype mappings and the algorithmic structure of evolution.Journal of the Royal Society, Interface · 2019Article
- The emergence of the two cell fates and their associated switching for a negative auto-regulating gene.BMC biology · 2019Article
- On the networked architecture of genotype spaces and its critical effects on molecular evolution.Open biology · 2018Review
- Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.Journal of the Royal Society, Interface · 2018Article
- Adding levels of complexity enhances robustness and evolvability in a multilevel genotype-phenotype map.Journal of the Royal Society, Interface · 2018Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Biological information is stored in DNA, RNA and protein sequences, which can be understood as genotypes that are translated into phenotypes. The properties of genotype-phenotype (GP) maps have been studied in great detail for RNA secondary structure. These include a highly biased distribution of genotypes per phenotype, negative correlation of genotypic robustness and evolvability, positive correlation of phenotypic robustness and evolvability, shape-space covering, and a roughly logarithmic scaling of phenotypic robustness with phenotypic frequency. More recently similar properties have been discovered in other GP maps, suggesting that they may be fundamental to biological GP maps, in general, rather than specific to the RNA secondary structure map. Here we propose that the above properties arise from the fundamental organization of biological information into 'constrained' and 'unconstrained' sequences, in the broadest possible sense. As 'constrained' we describe sequences that affect the phenotype more immediately, and are therefore more sensitive to mutations, such as, e.g. protein-coding DNA or the stems in RNA secondary structure. 'Unconstrained' sequences, on the other hand, can mutate more freely without affecting the phenotype, such as, e.g. intronic or intergenic DNA or the loops in RNA secondary structure. To test our hypothesis we consider a highly simplified GP map that has genotypes with 'coding' and 'non-coding' parts. We term this the Fibonacci GP map, as it is equivalent to the Fibonacci code in information theory. Despite its simplicity the Fibonacci GP map exhibits all the above properties of much more complex and biologically realistic GP maps. These properties are therefore likely to be fundamental to many biological GP maps.
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