IDEAS home Printed from https://ideas.repec.org/a/eee/thpobi/v79y2011i1p12-18.html
   My bibliography  Save this article

Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes

Author

Listed:
  • Rendel, Mark D.

Abstract

In RNA fitness landscapes with interconnected networks of neutral mutations, neutral precursor mutations can play an important role in facilitating the accessibility of epistatic adaptive mutant combinations. I use an exhaustively surveyed fitness landscape model based on short sequence RNA genotypes (and their secondary structure phenotypes) to calculate the minimum rate at which mutants initially appearing as neutral are incorporated into an adaptive evolutionary walk. I show first, that incorporating neutral mutations significantly increases the number of point mutations in a given evolutionary walk when compared to estimates from previous adaptive walk models. Second, that incorporating neutral mutants into such a walk significantly increases the final fitness encountered on that walk — indeed evolutionary walks including neutral steps often reach the global optimum in this model. Third, and perhaps most importantly, evolutionary paths of this kind are often extremely winding in their nature and have the potential to undergo multiple mutations at a given sequence position within a single walk; the potential of these winding paths to mislead phylogenetic reconstruction is briefly considered.

Suggested Citation

  • Rendel, Mark D., 2011. "Adaptive evolutionary walks require neutral intermediates in RNA fitness landscapes," Theoretical Population Biology, Elsevier, vol. 79(1), pages 12-18.
  • Handle: RePEc:eee:thpobi:v:79:y:2011:i:1:p:12-18
    DOI: 10.1016/j.tpb.2010.10.001
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0040580910000924
    Download Restriction: Full text for ScienceDirect subscribers only

    File URL: https://libkey.io/10.1016/j.tpb.2010.10.001?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Jeremy A. Draghi & Todd L. Parsons & Günter P. Wagner & Joshua B. Plotkin, 2010. "Mutational robustness can facilitate adaptation," Nature, Nature, vol. 463(7279), pages 353-355, January.
    2. W. Fontana & P. Schuster, 1998. "Continuity in Evolution: On the Nature of Transitions," Working Papers ir98039, International Institute for Applied Systems Analysis.
    3. Weissman, Daniel B. & Desai, Michael M. & Fisher, Daniel S. & Feldman, Marcus W., 2009. "The rate at which asexual populations cross fitness valleys," Theoretical Population Biology, Elsevier, vol. 75(4), pages 286-300.
    4. R Craig MacLean & Angus Buckling, 2009. "The Distribution of Fitness Effects of Beneficial Mutations in Pseudomonas aeruginosa," PLOS Genetics, Public Library of Science, vol. 5(3), pages 1-7, March.
    5. Walter Fontana & Peter Schuster, 1998. "Continuity in Evolution: On the Nature of Transition," Working Papers 98-04-030, Santa Fe Institute.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Miguel A Fortuna & Luis Zaman & Charles Ofria & Andreas Wagner, 2017. "The genotype-phenotype map of an evolving digital organism," PLOS Computational Biology, Public Library of Science, vol. 13(2), pages 1-20, February.
    2. Tobias Sikosek & Erich Bornberg-Bauer & Hue Sun Chan, 2012. "Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts," PLOS Computational Biology, Public Library of Science, vol. 8(9), pages 1-17, September.
    3. Krishnendu Chatterjee & Andreas Pavlogiannis & Ben Adlam & Martin A Nowak, 2014. "The Time Scale of Evolutionary Innovation," PLOS Computational Biology, Public Library of Science, vol. 10(9), pages 1-7, September.
    4. James P. Crutchfield & Erik van Nimwegen, 1999. "The Evolutionary Unfolding of Complexity," Working Papers 99-02-015, Santa Fe Institute.
    5. Jan Cupal & Stephan Kopp & Peter F. Stadler, 1999. "RNA Space Shape Technology," Working Papers 99-03-022, Santa Fe Institute.
    6. Roger D Kouyos & Gabriel E Leventhal & Trevor Hinkley & Mojgan Haddad & Jeannette M Whitcomb & Christos J Petropoulos & Sebastian Bonhoeffer, 2012. "Exploring the Complexity of the HIV-1 Fitness Landscape," PLOS Genetics, Public Library of Science, vol. 8(3), pages 1-9, March.
    7. Evandro Ferrada, 2014. "The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets," PLOS Computational Biology, Public Library of Science, vol. 10(12), pages 1-20, December.
    8. Proulx, Stephen R., 2011. "The rate of multi-step evolution in Moran and Wright–Fisher populations," Theoretical Population Biology, Elsevier, vol. 80(3), pages 197-207.
    9. Bårbel M. R. Stadler & Peter F. Stadler & Peter R. Wills, 2001. "Evolution in Systems of Ligation-Based Replicators," Working Papers 01-09-052, Santa Fe Institute.
    10. Campos, Paulo R.A & Adami, Christoph & Wilke, Claus O, 2002. "Optimal adaptive performance and delocalization in NK fitness landscapes," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 304(3), pages 495-506.
    11. Christian M. Reidys & Peter F. Stadler, 1998. "Neutrality in Fitness Landscapes," Working Papers 98-10-089, Santa Fe Institute.
    12. Sam F Greenbury & Steffen Schaper & Sebastian E Ahnert & Ard A Louis, 2016. "Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability," PLOS Computational Biology, Public Library of Science, vol. 12(3), pages 1-27, March.
    13. Osmond, Matthew M. & Otto, Sarah P., 2015. "Fitness-valley crossing with generalized parent–offspring transmission," Theoretical Population Biology, Elsevier, vol. 105(C), pages 1-16.
    14. Anne-Florence Bitbol & David J Schwab, 2014. "Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes," PLOS Computational Biology, Public Library of Science, vol. 10(8), pages 1-15, August.
    15. Serhii Aif & Nico Appold & Lucas Kampman & Oskar Hallatschek & Jona Kayser, 2022. "Evolutionary rescue of resistant mutants is governed by a balance between radial expansion and selection in compact populations," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    16. Michael D Nicholson & Tibor Antal, 2019. "Competing evolutionary paths in growing populations with applications to multidrug resistance," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-25, April.
    17. Rigato, Emanuele & Fusco, Giuseppe, 2020. "A heuristic model of the effects of phenotypic robustness in adaptive evolution," Theoretical Population Biology, Elsevier, vol. 136(C), pages 22-30.
    18. Alicia Sanchez-Gorostiaga & Djordje Bajić & Melisa L Osborne & Juan F Poyatos & Alvaro Sanchez, 2019. "High-order interactions distort the functional landscape of microbial consortia," PLOS Biology, Public Library of Science, vol. 17(12), pages 1-34, December.
    19. Alexander J. Stewart & Joshua B. Plotkin, 2015. "The Evolvability of Cooperation under Local and Non-Local Mutations," Games, MDPI, vol. 6(3), pages 1-20, July.
    20. Zeina Shreif & Vipul Periwal, 2014. "A Network Characteristic That Correlates Environmental and Genetic Robustness," PLOS Computational Biology, Public Library of Science, vol. 10(2), pages 1-23, February.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:eee:thpobi:v:79:y:2011:i:1:p:12-18. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Catherine Liu (email available below). General contact details of provider: https://www.journals.elsevier.com/intelligence .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.