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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.