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New structural variation in evolutionary searches of RNA neutral networks

Sumedha, Olivier C. Martin, Andreas Wagner
2007 Biosystems (Amsterdam. Print)  
Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets of RNA sequences that fold into the same structure.  ...  Our findings underscore the role of neutral networks in evolutionary innovation, and the role that high robustness can play in diminishing the potential for such innovation.  ...  New structural variation accumulates rapidly along a random walk of a neutral network We next examine how rapidly structural variation accumulates during a random walk on a neutral network.  ... 
doi:10.1016/j.biosystems.2006.11.007 pmid:17276586 fatcat:d67tsjalq5a2tgsmpizyn7rvvy

Robustness and evolvability: a paradox resolved

A. Wagner
2008 Proceedings of the Royal Society of London. Biological Sciences  
A consequence is that finite populations of sequences with a robust phenotype can access large amounts of phenotypic variation while spreading through a neutral network.  ...  In stark contrast, phenotype (structure) robustness promotes structure evolvability.  ...  In sum, in populations with both Nm[1 and Nm/1, an evolving population with a robust phenotype accesses more variation along its evolutionary path on a neutral network.  ... 
doi:10.1098/rspb.2007.1137 pmid:17971325 pmcid:PMC2562401 fatcat:kwzgyvbirrd4hghj7zi6tqdafm

The topology of evolutionary novelty and innovation in macroevolution

Douglas H. Erwin
2017 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Here I discuss the nature of evolutionary novelty and innovation within the context of evolutionary spaces, and argue that the primacy of search as a conceptual metaphor ignores the generation of new spaces  ...  One contribution of 16 to a theme issue 'Process and pattern in innovations from cells to societies'. Sewall Wright's fitness landscape introduced the concept of evolutionary spaces in 1932.  ...  Since many changes to a sequence will not generate a change in the folded structures, there will be large networks of effectively neutral changes.  ... 
doi:10.1098/rstb.2016.0422 pmid:29061895 pmcid:PMC5665810 fatcat:yanhuza6lbahdgd4cpulawblqy

Neutrality in evolutionary algorithms… What do we know?

Edgar Galván-López, Riccardo Poli, Ahmed Kattan, Michael O'Neill, Anthony Brabazon
2011 Evolving Systems  
Abstract Over the last years, the effects of neutrality have attracted the attention of many researchers in the Evolutionary Algorithms (EAs) community.  ...  Using as a framework the origin of neutrality and its study in different paradigms of EAs (e.g., Genetic Algorithms, Genetic Programming), we discuss the most significant works and findings on this topic  ...  This research is based upon works supported by Science Foundation Ireland under Grant No. 08/IN.1/I1868.  ... 
doi:10.1007/s12530-011-9030-5 fatcat:oiao7sjqnbh2bj45c4nwebv43u

The role of robustness in phenotypic adaptation and innovation

A. Wagner
2012 Proceedings of the Royal Society of London. Biological Sciences  
The second reason emerges from the evolutionary dynamics of evolving populations on genotype networks.  ...  In addition, robustness can help avoid an important evolutionary conflict between the interests of individuals and populations-a conflict that can impede evolutionary adaptation.  ...  The experiment asks whether cryptic variation can help a population find a new and superior genotype during an evolutionary search.  ... 
doi:10.1098/rspb.2011.2293 pmid:22217723 pmcid:PMC3282381 fatcat:6jke5smp6zbgfntvka4lio7t2q

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics [article]

Susanna Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalán, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio García-Martín, Paulien Hogeweg, Bhavin S. Khatri (+6 others)
2021 arXiv   pre-print
to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes.  ...  Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped  ...  Challenges in the computation of realistic genotypephenotype maps", which took place in Zaragoza (March 13th to March 15th, 2019) and triggered the production of this work.  ... 
arXiv:2002.00363v3 fatcat:iuqhuiwfczaqvjmadssrcm35ru

Genotypes with phenotypes: Adventures in an RNA toy world

Peter Schuster
1997 Biophysical Chemistry  
In order to nd at least one sequence for every common structures one need only search a (relatively) small part of sequence space.  ...  The existence of selectively neutral phenotypes plays an important role for the the success and the e ciency of evolutionary optimization.  ...  The dynamical concept of molecular evolution presented here was developed together with Drs. Walter Fontana, Christian Forst, Martijn Huynen, Christian Reidys, and Peter F. Stadler.  ... 
doi:10.1016/s0301-4622(97)00058-6 pmid:17029873 fatcat:fywom2rotrd6lak5teg22bseca

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

Susanna Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalán, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio García-Martín, Paulien Hogeweg, Bhavin S. Khatri (+6 others)
2021 Physics of Life Reviews  
to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes.  ...  Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped  ...  variation in determining evolutionary outcomes.  ... 
doi:10.1016/j.plrev.2021.03.004 pmid:34088608 fatcat:kdgh5d2g2bgclcluvbp5jndm3q

Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability [chapter]

Paulien Hogeweg
2012 Advances in Experimental Medicine and Biology  
RNA replicators, e.g. from sequence to folded structure and catalytic sites), in present-day organisms, the mapping itself is the result of evolution.  ...  Through genome, network, and dynamical structuring, the occurrence and/or effect of random mutations becomes nonrandom, and facilitates rapid adaptation.  ...  Acknowledgements I thank my (former) students, in particular Nobuto Takeuchi, Anton Crombach, Otto Corderro, and Thomas Cuypers.  ... 
doi:10.1007/978-1-4614-3567-9_10 pmid:22821460 fatcat:kmiytbvly5g55amkfkfxnfrkbq

Evolution in Silico and in Vitro: The RNA Model

P. Schuster
2001 Biological chemistry  
of extended neutral networks in genotype space.  ...  RNA evolution in vitro represents a basis for the development of a new and comprehensive model of evolution focusing on the phenotype and its fitness relevant properties.  ...  Fig. 5 : 5 Neutral networks in sequence space. The pre-image of the structure in the lower part of the figure is a connected neutral network spanning whole sequence space.  ... 
doi:10.1515/bc.2001.162 pmid:11688713 fatcat:g66rvr6zpnbvlpf4bdlzan2iqa

Experimental fitness landscapes to understand the molecular evolution of RNA-based life

Shreyas S Athavale, Brad Spicer, Irene A Chen
2014 Current Opinion in Chemical Biology  
This number has increased dramatically in the last several years, leading to qualitatively new investigations.  ...  However, the structure of fitness landscapes is essentially unknown.  ...  Acknowledgements We are grateful for support from the Simons Foundation (grant no. 290356), the Foundational Questions in Evolutionary Biology Fund (grant no.  ... 
doi:10.1016/j.cbpa.2014.09.008 pmid:25270912 fatcat:qekw2bvsh5ce5fivpx6a4l6yui

Smoothness within ruggedness: the role of neutrality in adaptation

M. A. Huynen, P. F. Stadler, W. Fontana
1996 Proceedings of the National Academy of Sciences of the United States of America  
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure.  ...  Secondary structure covers the major share of the free energy of tertiary structure formation and is frequently used to interpret RNA function and evolutionary data.  ...  (iii) Neutral networks of different structures are interwoven. While drifting on a neutral network, a population produces a fraction of mutants off the network and thereby explores new phenotypes.  ... 
doi:10.1073/pnas.93.1.397 pmid:8552647 pmcid:PMC40245 fatcat:p5tlw24x6bavjoppgjijwalniq

Motif frequency and evolutionary search times in RNA populations

Michael Stich, Susanna C. Manrubia
2011 Journal of Theoretical Biology  
Our results advance in the understanding of the distribution and attainability of RNA secondary structures.  ...  Furthermore, search and fixation processes are more efficient in a wider range of mutation rates for common structures, thus indicating that evolvability of RNA populations is not simply determined by  ...  position occupied by the neutral network of that structure in sequence space.  ... 
doi:10.1016/j.jtbi.2011.03.010 pmid:21419782 fatcat:u2knbuyizbhkdbowhug3c7x374

Neutral network sizes of biological RNA molecules can be computed and are not atypically small

Thomas Jörg, Olivier C Martin, Andreas Wagner
2008 BMC Bioinformatics  
We also study neutral set sizes of RNA structures in a publicly available database of functional, noncoding RNAs up to a length of 50 bases.  ...  Neutral networks or sets consist of all genotypes with a given phenotype.  ...  The size of a neutral set is a measure of a phenotype's rarity in sequence space. The greater this size, the easier it should be to find the phenotype in an evolutionary search.  ... 
doi:10.1186/1471-2105-9-464 pmid:18973652 pmcid:PMC2639431 fatcat:ok34myaxyjd2nl5e2pkcpjomh4

Innovation and robustness in complex regulatory gene networks

S. Ciliberti, O. C. Martin, A. Wagner
2007 Proceedings of the National Academy of Sciences of the United States of America  
Examples include the sequence (genotype) space of RNA and proteins and the secondary or tertiary structures (phenotypes) they form (15, 16) .  ...  We here address the problem of how robustness relates to innovation in a model system completely different from RNA, that of a transcriptional regulation network.  ...  Examples include the sequence (genotype) space of RNA and proteins and the secondary or tertiary structures (phenotypes) they form (15, 16) .  ... 
doi:10.1073/pnas.0705396104 pmid:17690244 pmcid:PMC1959426 fatcat:kqxpuetdrfcrpjzaeuh2odqjui
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