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 | Â |
Death rate | 0.5 | Â |
Initial # agents | 50 | Â |
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 | Â |
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 | Â |
Gene duplication | 0.006 | Note that with the gene, also its TFBS is duplicated |
Gene deletion | 0.009 | Â |
TFBS weight change | 0.001 | Â |
TFBS type change | 0.001 | Â |
TFBS duplication | 0.0015 | Â |
TFBS deletion | 0.004 | Â |
TFBS innovation | 0.001 | Spontaneous emergence of new TFBS |
Fitness | ||
G: penalty per gene | 0.0001 | Â |
T: penalty per TFBS | 0.00001 | Â |
Bonus for final tissue size | 0 or 0.1 | Per cell added by division |
Target size | 110 cells | Â |
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 |