3.1 A Basic SLiM Simulation

Our first simulation will be a lightly modified version of the script that comes up when we first open the SLiM graphical user interface (GUI). It is a simple simulation tracking one population, with no selection:

// set up a simple neutral simulation
initialize() {
    initializeMutationRate(1e-7);
    
    // m1 mutation type: neutral
    initializeMutationType("m1", 0.5, "f", 0.0);
    
    // g1 genomic element type: uses m1 for all mutations
    initializeGenomicElementType("g1", m1, 1.0);
    
    // uniform chromosome of length 100 kb with uniform recombination
    initializeGenomicElement(g1, 0, 99999);
    initializeRecombinationRate(1e-8);
}

// create a population of 500 individuals
1 early() {
    sim.addSubpop("p1", 500);
}

2000 late() { 
  sim.outputFixedMutations(); 
}