Smoothness Within Ruggedness: the Role of Neutrality in Adaptation

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1996 Jan 9

PMID 8552647

Citations 121

Authors

M A Huynen

P F Stadler

W Fontana

Affiliations

Soon will be listed here.

Abstract

RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks, evolving populations split into subpopulations, which diffuse independently in sequence space. This demands a distinction between two mutation thresholds: one at which genotypic information is lost and one at which phenotypic information is lost. In between, diffusion enables the search of vast areas in genotype space while still preserving the dominant phenotype. By this dynamic the success of phenotypic adaptation becomes much less sensitive to the initial conditions in genotype space.

Citing Articles

Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole to triphosphate activation.

DasGupta S, Weiss Z, Nisler C, Szostak J Proc Natl Acad Sci U S A. 2024; 121(38):e2407325121.

PMID: 39269776 PMC: 11420214. DOI: 10.1073/pnas.2407325121.

Non-Poissonian Bursts in the Arrival of Phenotypic Variation Can Strongly Affect the Dynamics of Adaptation.

Martin N, Schaper S, Camargo C, Louis A Mol Biol Evol. 2024; 41(6).

PMID: 38693911 PMC: 11156200. DOI: 10.1093/molbev/msae085.

Physics of diffusion in viral genome evolution.

Manrubia S, Cuesta J Proc Natl Acad Sci U S A. 2023; 120(34):e2310999120.

PMID: 37556488 PMC: 10450443. DOI: 10.1073/pnas.2310999120.

RNA aptamers for AMPA receptors.

Huang Z, Niu L Neuropharmacology. 2021; 199:108761.

PMID: 34509496 PMC: 9284364. DOI: 10.1016/j.neuropharm.2021.108761.

Neutral quasispecies evolution and the maximal entropy random walk.

Smerlak M Sci Adv. 2021; 7(16).

PMID: 33853768 PMC: 8046360. DOI: 10.1126/sciadv.abb2376.

References

Komiyama N, Miyazaki G, Tame J, Nagai K . Transplanting a unique allosteric effect from crocodile into human haemoglobin. Nature. 1995; 373(6511):244-6. DOI: 10.1038/373244a0. View

Beaudry A, Joyce G . Directed evolution of an RNA enzyme. Science. 1992; 257(5070):635-41. DOI: 10.1126/science.1496376. View

Putz J, Puglisi J, Florentz C, Giege R . Identity elements for specific aminoacylation of yeast tRNA(Asp) by cognate aspartyl-tRNA synthetase. Science. 1991; 252(5013):1696-9. DOI: 10.1126/science.2047878. View

Schuster P, Fontana W, Stadler P, Hofacker I . From sequences to shapes and back: a case study in RNA secondary structures. Proc Biol Sci. 1994; 255(1344):279-84. DOI: 10.1098/rspb.1994.0040. View

Sneath P . Some thoughts on bacterial classification. J Gen Microbiol. 1957; 17(1):184-200. DOI: 10.1099/00221287-17-1-184. View

Fontana , Schnabl , SCHUSTER . Physical aspects of evolutionary optimization and adaptation. Phys Rev A Gen Phys. 1989; 40(6):3301-3321. DOI: 10.1103/physreva.40.3301. View

Berek C, Ziegner M . The maturation of the immune response. Immunol Today. 1993; 14(8):400-4. DOI: 10.1016/0167-5699(93)90143-9. View

Bonhoeffer S, McCaskill J, Stadler P, Schuster P . RNA multi-structure landscapes. A study based on temperature dependent partition functions. Eur Biophys J. 1993; 22(1):13-24. DOI: 10.1007/BF00205808. View

Sassanfar M, Szostak J . An RNA motif that binds ATP. Nature. 1993; 364(6437):550-3. DOI: 10.1038/364550a0. View

10.

Zuker M, Stiegler P . Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981; 9(1):133-48. PMC: 326673. DOI: 10.1093/nar/9.1.133. View

11.

Kimura M . Evolutionary rate at the molecular level. Nature. 1968; 217(5129):624-6. DOI: 10.1038/217624a0. View

12.

Levisohn R, Spiegelman S . Further extracellular Darwinian experiments with replicating RNA molecules: diverse variants isolated under different selective conditions. Proc Natl Acad Sci U S A. 1969; 63(3):805-11. PMC: 223524. DOI: 10.1073/pnas.63.3.805. View

13.

Mills D, Peterson R, Spiegelman S . An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc Natl Acad Sci U S A. 1967; 58(1):217-24. PMC: 335620. DOI: 10.1073/pnas.58.1.217. View

14.

Eigen M . Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften. 1971; 58(10):465-523. DOI: 10.1007/BF00623322. View

15.

Shapiro B, Zhang K . Comparing multiple RNA secondary structures using tree comparisons. Comput Appl Biosci. 1990; 6(4):309-18. DOI: 10.1093/bioinformatics/6.4.309. View

16.

Robertson D, Joyce G . Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature. 1990; 344(6265):467-8. DOI: 10.1038/344467a0. View

17.

Joyce G . Amplification, mutation and selection of catalytic RNA. Gene. 1989; 82(1):83-7. DOI: 10.1016/0378-1119(89)90033-4. View

18.

Ellington A, Szostak J . In vitro selection of RNA molecules that bind specific ligands. Nature. 1990; 346(6287):818-22. DOI: 10.1038/346818a0. View