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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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Multiplicity of phenotypes and RNA evolution.

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RNA sequences can evolve continuously. Quasineutral mutations, which allow RNA to adopt multiple structures, bridge neutral and random evolutionary walks, supporting the continuous nature of evolution.

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Area of Science:

  • Evolutionary Biology
  • Molecular Biology
  • Bioinformatics

Background:

  • Motoo Kimura's neutral theory posits evolution is driven by neutral mutations.
  • RNA's dual genotype-phenotype nature makes it ideal for studying neutrality.
  • Neutral networks are sets of RNA sequences with identical phenotypes, crucial for neutral evolution.

Purpose of the Study:

  • To investigate the impact of the one-to-many genotype-to-phenotype map in RNA on neutral theory.
  • To explore the concept of quasineutrality in RNA evolution.
  • To analyze how quasineutral walks traverse phenotype space.

Main Methods:

  • Analysis of RNA genotype-to-phenotype mapping, noting 29.5% of sequences yield multiple phenotypes.
  • Definition of quasineutral genotypes as those sharing at least one phenotype.
  • Simulating evolutionary walks in genotype space using quasineutral steps.

Main Results:

  • Quasineutral mutations exhibit energy profiles similar to neutral mutations.
  • Quasineutral walks can percolate phenotype space, connecting neutral and random walks.
  • These walks demonstrate a continuous evolutionary process and transitions between neutral networks.

Conclusions:

  • The one-to-many genotype-to-phenotype map significantly influences RNA evolution.
  • Quasineutrality provides a mechanism for continuous evolution, bridging neutral and random drift.
  • This study offers new insights into the dynamics of neutral evolution in RNA.