neutral_contraction.slim

// Instantaneous population contraction from 1000 to 250 at genneration 2000
initialize()
{
	// set the overall mutation rate
	initializeMutationRate(1e-5);
	
	// 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);
	
	// Chromosome of length 10 kb, homogenous (all of type g1)
	initializeGenomicElement(g1, 0, 9999);
	
	// uniform recombination along the chromosome
	initializeRecombinationRate(1e-8);
}

// create a population of 1000 individuals 
1 early()
{
	sim.addSubpop("p1", 1000);
}
// at generation 2000 decrease the population size to 250 immediately

2000 early() { p1.setSubpopulationSize(250); }

// run to generation 5000
5000 late() {

// randomly subsample 20 individuals for output
allIndividuals = sim.subpopulations.individuals;
 sampledIndividuals = sample(allIndividuals, 20);
 sampledIndividuals.genomes.outputVCF();

}