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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