title: Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.
abstract: BACKGROUND
  The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered.
  
  
  RESULTS
  The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape.
  
  
  CONCLUSIONS
  Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.
authors.affiliation: Department of Computer Science, University of A Coruña, Campus de Elviña s/n, A Coruña, 15071, Spain. jose.santos@udc.es.
authors.forename: José
authors.initials: J
authors.lastname: Santos
authors.affiliation: Department of Computer Science, University of A Coruña, Campus de Elviña s/n, A Coruña, 15071, Spain.
authors.forename: Ángel
authors.initials: Á
authors.lastname: Monteagudo
mesh_terms: D000465:Algorithms; D005075:Biological Evolution; D003062:Codon; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics*; D008957:Models, Genetic; D012641:Selection, Genetic
chemical_list: D003062:Codon
keywords: Evolutionary computing; Fitness sharing; Genetic algorithm; Genetic code adaptability