Figure 1.

Individual-based model of co-evolving TEs and host genomes. (a) Individuals are cells that undergo a process of birth, death and DNA uptake on a spatial grid. Packaged within cells are genomes with three types of genetic elements. A total of 10 host-essential genes (a–j, in any given order) are necessary for cell viability. There is no explicit cost on the size of the genome, meaning that multiple (redundant) copies of genes may exist, as well as large stretches of non-coding DNA. The genomes also encode TEs that replicate through transposition independent of the host genome. Transposition of TEs happens both after uptake of eDNA (HGT) and during the lifetime of each cell. When transposons insert into coding genes (a host-essential gene or another TE), that gene is inactivated and replaced by a non-coding element. A small fitness cost (c = 0.005) is associated with each extra TE copy. The transposition rate of TEs is denoted as φ, and may differ among individual TEs. (b) Different mutations are depicted for cartoon genomes. Genomes are scanned from left to right upon reproduction, and each position may undergo mutation (illustrated in the cartoon with a white arrow). Mutations generate variation in genome size and gene content of individual cells. Large-scale duplications and deletions affect, on average, 25% of the genome and ensure that genomes do not expand indefinitely (see [30]). As mutations also operate on the level of TEs (i.e., modifying φ), the resulting model describes a multi-level coevolutionary process.