Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces

On 13 November, 2014

wtnn-rnaRobustness and evolvability are highly intertwined properties of biological systems. The relationship between these properties determines how biological systems are able to withstand mutations and show variation in response to them. Computational studies have explored the relationship between these two properties using neutral networks of RNA sequences (genotype) and their secondary structures (phenotype) as a model system. However, these studies have assumed every mutation to a sequence to be equally likely; the differences in the likelihood of the occurrence of various mutations, and the consequence of probabilistic nature of the mutations in such a system have previously been ignored. Associating probabilities to mutations essentially results in the weighting of genotype space. We here perform a comparative analysis of weighted and unweighted neutral networks of RNA sequences, and subsequently explore the relationship between robustness and evolvability.

We show that assuming an equal likelihood for all mutations (as in an unweighted network), underestimates robustness and overestimates evolvability of a system. In spite of discarding this assumption, we observe that a negative correlation between sequence (genotype) robustness and sequence evolvability persists, and also that structure (phenotype) robustness promotes structure evolvability, as observed in earlier studies using unweighted networks. We also study the effects of base composition bias on robustness and evolvability. Particularly, we explore the association between robustness and evolvability in a sequence space that is AU-rich – sequences with an AU content of 80% or higher, compared to a normal (unbiased) sequence space. We find that evolvability of both sequences and structures in an AU-rich space is lesser compared to the normal space, and robustness higher. We also observe that AU-rich populations evolving on neutral networks of phenotypes, can access less phenotypic variation compared to normal populations evolving on neutral networks.

Original Paper: 

  • [DOI] R. Partha and K. Raman, “Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces,” PLoS ONE, vol. 9, iss. 11, p. e112792+, 2014.
    [bibtex]
    @article{Partha2014Revisiting,
      abstract = {Robustness and evolvability are highly intertwined properties of biological systems. The relationship between these properties determines how biological systems are able to withstand mutations and show variation in response to them. Computational studies have explored the relationship between these two properties using neutral networks of {RNA} sequences (genotype) and their secondary structures (phenotype) as a model system. However, these studies have assumed every mutation to a sequence to be equally likely; the differences in the likelihood of the occurrence of various mutations, and the consequence of probabilistic nature of the mutations in such a system have previously been ignored. Associating probabilities to mutations essentially results in the weighting of genotype space. We here perform a comparative analysis of weighted and unweighted neutral networks of {RNA} sequences, and subsequently explore the relationship between robustness and evolvability. We show that assuming an equal likelihood for all mutations (as in an unweighted network), underestimates robustness and overestimates evolvability of a system. In spite of discarding this assumption, we observe that a negative correlation between sequence (genotype) robustness and sequence evolvability persists, and also that structure (phenotype) robustness promotes structure evolvability, as observed in earlier studies using unweighted networks. We also study the effects of base composition bias on robustness and evolvability. Particularly, we explore the association between robustness and evolvability in a sequence space that is {AU}-rich – sequences with an {AU} content of 80\% or higher, compared to a normal (unbiased) sequence space. We find that evolvability of both sequences and structures in an {AU}-rich space is lesser compared to the normal space, and robustness higher. We also observe that {AU}-rich populations evolving on neutral networks of phenotypes, can access less phenotypic variation compared to normal populations evolving on neutral networks.},
      added-at = {2018-12-02T16:09:07.000+0100},
      author = {Partha, Raghavendran and Raman, Karthik},
      biburl = {https://www.bibsonomy.org/bibtex/2124b29e36d14280222afd19457b34aad/karthikraman},
      day = 12,
      doi = {10.1371/journal.pone.0112792},
      interhash = {5a3aa793e4b4ab6e5e91429698317c65},
      intrahash = {124b29e36d14280222afd19457b34aad},
      journal = {PLoS ONE},
      keywords = {evolvability myown neutral\_networks robustness},
      month = nov,
      number = 11,
      pages = {e112792+},
      posted-at = {2014-11-13 20:16:45},
      priority = {2},
      timestamp = {2019-02-10T16:15:28.000+0100},
      title = {Revisiting Robustness and Evolvability: Evolution in Weighted Genotype Spaces},
      url = {http://dx.doi.org/10.1371/journal.pone.0112792},
      volume = 9,
      year = 2014
    }

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