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Table 1 Parameter values used for the runs detailed in the Results section

From: In silico experimental evolution: a tool to test evolutionary scenarios

Parameter Symbol Value
Population size N 1,000
Size of the initial (random) genome L init 5,000 base pairs
Promoter sequence   0101011001110010010110,
with up to dmax = 4 mismatches
Terminator sequences   abcd*** d ¯ c ¯ b ¯ a ¯
Initiation signal for the translation   011011****000
Termination signal for the translation   001
Genetic code   See Figure 1
Global set of "cellular processes" Ω [0,1]
Maximal pleiotropy of the proteins w max 5.10-3
Environmental target fluctuates around... f ¯ E See Figure 1
Environmental fluctuations: characteristic time τ 2,500
Environmental fluctuations: standard deviation σ 5.10-3
Selection intensity k 750 initially, then 250
Point mutation rate u point 5.10-6 per bp
Small insertion rate u smallins 5.10-6 per bp
Small deletion rate u smalldel 5.10-6 per bp
Large deletion rate u largedel 5.10-5 per bp
Duplication rate u duplic 5.10-5 per bp
Inversion rate u inv 5.10-5 per bp
Translocation rate u transloc 5.10-5 per bp
Length of small indels   Uniform law bw. 1 and 6 bp
  1. These parameter values were chosen after preliminary analyses. Some parameters like the structural signals have been shown not to impact the genome structure. The impact of w max has been studied [30] as well as the impact of mutation rates and particularly rearrangement rates [26]. Here, the mutation rates and w max values were chosen to obtain a gene density close to bacterial gene density and with enough genes to allow experiments on reductive genome evolution. The intensity and frequency of environmental variations (σ and τ respectively) are currently under study; k is tested here.