const-Ne-10000_single-pulse_t-m-s.slim

// single-pulse admixture simulation for N=10000
// user specifies:
// *timing of selection onset
// *selection coefficient 
// *total number of generations
// *P1 admixture contribution
// *outfile directory/name
// usage: slim -d s=s -d mig=m -d tsel=t -d tend=gen -d pos=pos -d out='"out"' const-Ne-10000_single-pulse_t-m-s.slim 

initialize() {
	defineConstant("L", 1e8); // 100Mb chromosome
	initializeTreeSeq();
	initializeMutationRate(0);
	initializeMutationType("m1", 0.5, "f", 0);
	initializeGenomicElementType("g1", m1, 1.0);
	initializeGenomicElement(g1, 0, L);
	initializeRecombinationRate(1e-8); 		// uniform recombination rate
}

1 {
	selstart = asInteger(tsel); 			// set timing of selection onset
	genend = asInteger(tend); 			// set total number of generations
	sim.rescheduleScriptBlock(s1, start=1*selstart);
	sim.rescheduleScriptBlock(s2, 1*genend, 1*genend);
}

//source populations each have 1 diploid individual

1 late() {
	sim.addSubpop("p1", 1);
	sim.addSubpop("p2", 1);
	sim.treeSeqRememberIndividuals(sim.subpopulations.individuals);
	locus = asInteger(pos); 			// set variant position
	p1.genomes.addNewDrawnMutation(m1, locus);
	
	sim.addSubpop("p3", 10000);
	m = asFloat(mig);				// set admixture proportion
	p3.setMigrationRates(c(p1, p2), c(m, 1-m));
}

2 late() {
	p3.setMigrationRates(c(p1, p2), c(0.0, 0.0));
	p1.setSubpopulationSize(0);
	p2.setSubpopulationSize(0);
}

s1 1000 late() {
	mut = sim.mutationsOfType(m1);
	mut.setSelectionCoeff(s);			// set selection coefficient
}

s2 1000 late() {
	outname = "" + out + ".trees";
	sim.treeSeqOutput(outname);
	sim.simulationFinished();
}