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Table 1 Parameter values

From: In silico evo-devo: reconstructing stages in the evolution of animal segmentation

Parameter Values Remarks
General
Grid size 30 × 30  
Evolutionary time steps 50,000  
Death rate 0.5  
Initial # agents 50  
Development
Developmental time steps 240 The number of integration steps
Integration step size 1 Fourth-order Runge–Kutta integration
Morphogen decay rate 0.2 Only for persistent posterior morphogen of which 9 form the head
Initial tissue size 10 cells  
Gene and protein dynamics
Gene product decay rate 0.05–0.9  
Hill constant of the TFBS 10–400  
Gene transcription 10–100  
Mutational dynamics
Nr of gene types 16  
Gene duplication 0.006 Note that with the gene, also its TFBS is duplicated
Gene deletion 0.009  
TFBS weight change 0.001  
TFBS type change 0.001  
TFBS duplication 0.0015  
TFBS deletion 0.004  
TFBS innovation 0.001 Spontaneous emergence of new TFBS
Fitness
G: penalty per gene 0.0001  
T: penalty per TFBS 0.00001  
Bonus for final tissue size 0 or 0.1 Per cell added by division
Target size 110 cells  
Penalty for exceeding target size 1 For each cell more than target size
Control period 20 steps Period over which gene expression stability and sometimes number of late-stage divisions is measured
U: expression variance penalty 0.1 Penalty per cell that has a variance in segmentation gene level >5.0 during the control period