basic model - KamilSJaron/reproductive_mode_TE_dynamics GitHub Wiki

The first draft simulation took naively all the parameters as mentioned above (simulation 004. Selection model is slightly less trivial than the other parameters, therefore it's described in section bellow.

The only obvious discrepancy to real asexual yeast genome is number of chromosomes, I used 2 instead of 16. I left 200 Te slots per chromosome and modeled diploid genome, therefore there is very big margin in terms of genome space.

The modeled decrease is ~6 copies, which is slightly less that what was expected from real data, but it's a great success given how crude the biological estimates of all the parameters might be.

Here is number of TE copies of 10 replicates over 990 simulated generations

However, such model is dependent only wish selection since the transposition rate is the same as excision rate. That is confirmed also by a simulation with sex every 90 generations (simulation 003, because in that simulation loss of transposable elements is much faster

Either the model is too simple to capture reality, or the parameters derived from the lab are unrealistic. We expect to find out conditions for which sexual won't lose any TEs over the 990 generations (equilibrium simulation). We were performed a set of simulation where we were incrementally increasing transposition rate (simulations sims/005 - 012). Eventually we found a transposition rate (u = 0.004) that generates a simulation where number of TEs oscillates around equilibria (simulation 013). We use the same parameters for a simulation without sexual reproduction every 90 generations (simulation 015). Unlike sexual simulation, asexuals were accumulating TEs

, suggesting that the model is unlikely sufficiently complex to capture reality of transposable elements.