ModelA.slim

// set up a simulation
initialize()
{
	// set the overall mutation rate
	initializeMutationRate(5.468928e-08);
	// we use autosomes not sex chromosomes, therefore:
	initializeSex("A");
	// two types of mutations: deleterious and neutral
	// Neutral mutation (synonymous sites)
	initializeMutationType("m1", 0.5, "f", 0.0);
	// detrimental mutations (nonsynonymous sites) following a gamma distribution with mean=-2.5, shape=0.3
	initializeMutationType("m2", 0.1, "g", -2.5, 0.35);
	// g1 genomic element type: coding: 
	// Now I initialize the coding element with 2/3 non-synonymous and 1/3 synonymous
	initializeGenomicElementType("g1", c(m1, m2), c(0.34,0.66));
	// chromosome consisting of 1500 genomic elements of type g1 , with gaps between them at regular intervals
	for (index in 1:1500)
		initializeGenomicElement(g1, index*1000, index*1000 + 499);
	// uniform recombination rate 
	// this value needs a better estimate
	initializeRecombinationRate(6.604764e-06);
}
1 { sim.addSubpop("p1", 10000); }
50000 {  p1.setSubpopulationSize(20000); }
65000 late() {sim.addSubpopSplit("p2", 20000, p1);}
65001{
		
	p1.setSubpopulationSize(1000);
	p2.setSubpopulationSize(30000);
}
71001 late() {
	
	p1.outputSample(60,filePath="SmallPop_mutations_ModelA.txt",append=F);
	p2.outputSample(60,filePath="LargePop_mutationss_ModelA.txt",append=F);
	sim.outputFixedMutations(filePath="All_substitutionss_ModelA.txt",append=F);
}