Continuity in Evolution: On the Nature of Transitions
SciencePublished 29 May 1998
Walter Fontana, Peter Schuster
Citations468
SJR quartileQ1
SJR score10.42
SNIP6.62
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
Abstract
To distinguish continuous from discontinuous evolutionary change, a relation of nearness between phenotypes is needed. Such a relation is based on the probability of one phenotype being accessible from another through changes in the genotype. This nearness relation is exemplified by calculating the shape neighborhood of a transfer RNA secondary structure and provides a characterization of discontinuous shape transformations in RNA. The simulation of replicating and mutating RNA populations under selection shows that sudden adaptive progress coincides mostly, but not always, with discontinuous shape transformations. The nature of these transformations illuminates the key role of neutral genetic drift in their realization.
Keywords
Biochemistry, Genetics and Molecular Biology
ScienceSystematic Evolution of Ligands by Exponential Enrichment: RNA Ligands to Bacteriophage T4 DNA Polymerase
10,359 Citations1990Craig Tuerk, Larry Gold
Nucleic Acids ResearchOptimal computer folding of large RNA sequences using thermodynamics and auxiliary information
3,628 Citations1981Michael Zuker, Patrick Stiegler
A new computer method for folding an RNA molecule that finds a conformation of minimum free energy using published values of stacking and destabilizing energies and is much more efficient, faster, and can fold larger molecules than procedures which have appeared up to now in the biological literature.
Monatshefte für Chemie - Chemical MonthlyFast folding and comparison of RNA secondary structures
2,343 Citations1994Ivo L. Hofacker, Walter Fontana +4 more
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and base pairing probabilities.
Proceedings of the National Academy of SciencesSmoothness within ruggedness: the role of neutrality in adaptation.
562 Citations1996Martijn A. Huynen, Peter F. Stadler +1 more
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure, on which the success of phenotypic adaptation becomes much less sensitive to the initial conditions in genotype space.
Proceedings of the National Academy of SciencesCoaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
472 Citations1994A E Walter, Douglas H. Turner +5 more
An RNA model system consisting of an oligomer binding to a 4-nt overhang at the 5' end of a hairpin stem provides thermodynamic parameters for helix-helix interfaces and predictions of 11 RNA secondary structures improve from 67 to 74% accuracy by inclusion of similar stacking contributions.
SciencePunctuated Evolution Caused by Selection of Rare Beneficial Mutations
355 Citations1996Santiago F. Elena, Vaughn S. Cooper +1 more
A clear and unambiguous case of punctuated evolution is presented for cell size in a population of Escherichia coli evolving for 3000 generations in a constant environment.
Journal of Molecular EvolutionExploring phenotype space through neutral evolution
211 Citations1996Martijn A. Huynen
This work has shown that neutral evolution explores phenotype space and can play a role in adaptation and gives access to a virtually unlimited number of secondary structures that are a single point mutation from the neutral path.
Biophysical ChemistryA computer model of evolutionary optimization
204 Citations1987Walter Fontana, Peter Schuster
A chemical reaction model which considers RNA replication including correct copying and point mutations together with hydrolytic degradation and the dilution flux of a flow reactor is analysed in order to investigate some basic features of evolutionary optimization dynamics.
Monatshefte für Chemie - Chemical MonthlyAnalysis of RNA sequence structure maps by exhaustive enumeration I. Neutral networks
141 Citations1996W. Gr�ner, Robert Giegerich +6 more
Biophysical ChemistryGenotypes with phenotypes: Adventures in an RNA toy world
50 Citations1997Peter Schuster
Molecular evolution found a highly promising technological application in the design of biomolecules with predefined properties, and the existence of selectively neutral phenotypes plays an important role for the the success and the efficiency of evolutionary optimization.