Table 1.
List of model parameters and values (unless stated otherwise). Mutational parameters (marked by an asterisk) are disabled for figure 2.
| parameter | value | description |
|---|---|---|
| grid size (W, H) | 150,150 | size of (toroidal) grid on which individuals reside |
| number of host-essential functions | 10 | the number of unique functions that a cell must perform to be viable (i.e. the minimal genome size is equal to 10) |
| fitness penalty per TE (c) | 0.005 | per-TE penalty on fitness |
| natural death rate (d) | 0.02 | probability of stochastic death for individual cells |
| DNA uptake (u) | 0.01 | probability of uptake per (local) fragment of DNA (after uptake, the chance of successful integration is determined by the φ-parameter of the TE) |
| rate of transposition events within genomes (j) | 0.01 | probability of transposition-event during the lifetime of a cell (after this event has been invoked, the chance of successful transposition is further determined by the φ-parameter of the TE) |
| DNA diffusion (D) | 0.01 | probability of fragments moving into a random neighbouring grid point |
| DNA degradation (q) | 0.02 | probability of fragments being removed from the grid |
| TE transposition rate (φ) | 0.9/evolvable | individual success-rate of transposition (can be unique/evolvable per TE) |
| TE-induced damage (b) | 1.0 | when a TE inserts into the list of DNA elements (the genome), the adjacent coding genes get inactivated with this probability (otherwise, it is assumed to insert next to it without damaging the gene) |
| single-gene duplication/deletion* | 0.001 per position | per gene per generation probability of duplication or deletion |
| large scale duplication/deletion/inversion* | 0.001 per position | per gene per generation probability of position invoking a large-scale duplication, deletion, or inversion |
| gene inactivation* | 0.001 per position | per gene per generation probability of gene inactivation (position becomes non-coding) |
| TE transposition mutation* | 0.01 per TE | for every TE replication (transposition, host-genome replication), the probability that the transposition rate changes with a uniform step size of ±0.1 |