Determinants of simulated RNA evolution. Journal Article


Author(s): Kupczok, Anne; Dittrich, Peter
Article Title: Determinants of simulated RNA evolution.
Affiliation
Abstract: Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search.
Journal Title: Journal of Theoretical Biology
Volume: 238
Issue 3
ISSN: 0022-5193
Publisher: Elsevier  
Date Published: 2006-01-01
Start Page: 726
End Page: 35
DOI: 10.1016/j.jtbi.2005.06.019
Open access: no
IST Austria Authors
  1. Anne Kupczok
    10 Kupczok