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CostaRica_outcrossing_additive.slim.txt
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CostaRica_outcrossing_additive.slim.txt
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// Costa Rica, additive mutations, no inbreeding
initialize() {
initializeSLiMOptions(keepPedigrees=T);
defineConstant("seqLength", 10000000);
defineConstant("Lns_over_Ls", 2.31);
defineConstant("ROHcutoff", 1000000);
defineConstant("simScalFac", 1);
defineConstant("sampleSize", 60);
initializeMutationRate(1.5e-8*simScalFac);
initializeRecombinationRate(1e-8*simScalFac);
// m1 mutation type: neutral
initializeMutationType("m1", 0.5, "f", 0.0);
initializeMutationType("m2", 0.5, "g", -0.028*simScalFac, 0.19);
m2.convertToSubstitution = T;
// g1 genomic element type: uses m1 for all mutations
initializeGenomicElementType("g1", c(m1, m2), c(1,Lns_over_Ls));
initializeGenomicElementType("g2", m1, 1);
initializeGenomicElementType("g3", m1, 1);
// Generate random genes along the chromosome
base = 0;
nc_length_total = 0;
in_length_total = 0;
ex_length_total = 0;
while (base < seqLength) {
// make a non-coding region
nc_length = asInteger(runif(1, 100, 5000)); nc_length_total = nc_length_total + nc_length;
initializeGenomicElement(g2, base, base + nc_length - 1);
base = base + nc_length;
// make first exon
ex_length = asInteger(rlnorm(1, log(50), log(2))) + 1; ex_length_total = ex_length_total + ex_length;
initializeGenomicElement(g1, base, base + ex_length - 1);
base = base + ex_length;
// make additional intron-exon pairs
do {
in_length = asInteger(rlnorm(1, log(100), log(1.5))) + 10; in_length_total = in_length_total + in_length;
initializeGenomicElement(g3, base, base + in_length - 1);
base = base + in_length;
ex_length = asInteger(rlnorm(1, log(50), log(2))) + 1; ex_length_total = ex_length_total + ex_length;
initializeGenomicElement(g1, base, base + ex_length - 1);
base = base + ex_length;
} while (runif(1) < 0.8); // 20% probability of stopping
}
// final non-coding region
nc_length = asInteger(runif(1, 100, 5000));
initializeGenomicElement(g2, base, base + nc_length - 1);
// define some constants that will be used later for calculating summary statistics
defineConstant("in_length_total_c", in_length_total);
defineConstant("ex_length_total_c", ex_length_total);
defineConstant("nc_length_total_c", nc_length_total);
}
//Native Americans of Costa Rica
1 {
cat("# gen popSize sampleSize mutLoad mutLoadFixed fitness numNeutral numNS numFixedNS Pneutral PNS meanTotalROH NeutralInROH NSInROH NeutralNotInROH NSNotInROH F" + "\n");
// save this run's identifier, used to save and restore
defineConstant("simID", getSeed());
sim.addSubpop("p1", 10000);
sim.tag = 0;
}
70000 {
m2.convertToSubstitution = F;
p1.setSubpopulationSize(2000);
}
70167 {
sim.addSubpopSplit("p2", 2000, p1);
}
70834 {
p2.setSubpopulationSize(10000);
}
71500 {
p1.setSubpopulationSize(10000);
}
71650 {
p1.setSubpopulationSize(1000);
}
71651 {
p1.setMigrationRates(p2, 0.7);
}
71652 {
p1.setMigrationRates(p2, 0.0);
// p1.setSelfingRate(0.182); // Start inbreeding by selfing...
}
// 71652:71667 mateChoice() { // Inbreeding with 50% probability
// if (runif(1) < 0.50) {
// weights * ifelse(individual.relatedness(sourceSubpop.individuals) >= 0.25 & individual.relatedness(sourceSubpop.individuals) != 1.0 , 1.0 , 0.00001);
// }
// else {
// weights;
// }
// }
71653 {
p2.setSubpopulationSize(0);
}
71660 {
p1.setSubpopulationSize(10000);
// p1.setSelfingRate(0); // Stop inbreeding by selfing...?
}
71667 {sim.simulationFinished();}
// output samples of 50 genomes periodically, all fixed mutations at end
66667:71667 late() {
if ((sim.generation % 100 == 0 & sim.generation < 71567) | sim.generation >= 71567) {
// Population scale statistics of p1
meanFitness = mean(p1.cachedFitness(NULL));
i = p1.individuals;
mdel = i.genomes.mutations[i.genomes.mutations.mutationType == m2];
mutLoad = mdel.size()/i.size();
mdel_uniq = unique(mdel);
mdel_uniq_fixedID = apply(mdel_uniq, "sum(mdel == applyValue) == i.genomes.size();");
numFixedDel = sum(mdel_uniq_fixedID);
mutLoad_fixed = numFixedDel * 2;
// Inbreeding F
mneut_uniq = unique(i.genomes.mutations[i.genomes.mutations.mutationType == m1]);
freq = sim.mutationFrequencies(p1, mneut_uniq); // freq of neut mutations in p1
ID = freq>0.05 & freq<0.95; // Apply a frequency cutoff of MAF>5%
expHetPerSite = (4*i.size()^2*freq*(1-freq)/(2*i.size()-1))[ID]; // According to Hedrick book p. 92
obsHetPerSite = apply(mneut_uniq[ID], "firstChr = i.genomes.containsMutations(applyValue)[seq(0,i.genomes.size()-2,2)]; secondChr = i.genomes.containsMutations(applyValue)[seq(1,i.genomes.size()-1,2)]; numHets = sum((asInteger(firstChr) + asInteger(secondChr)) == 1); return(numHets);");
inbreedF = mean(1-obsHetPerSite/expHetPerSite);
// Sample scale statistics
i = sample(p1.individuals, sampleSize, F);
m = sortBy(i.genomes.mutations, "position");
m_uniq = unique(m);
DAF = apply(m_uniq, "sum(m == applyValue);");
m_uniq_polym = m_uniq[DAF != i.genomes.size()];
NS_mut_in_sample = sum(i.countOfMutationsOfType(m2));
ROH_length_sumPerInd = c();
NS_mut_perInd = c();
Neutral_mut_perInd = c();
NS_mut_in_ROH_perInd = c();
Neutral_mut_in_ROH_perInd = c();
for (individual in i) {
indm = sortBy(individual.genomes.mutations, "position");
indm = indm[match(indm, m_uniq_polym) >= 0]; // Check that individual mutations are not fixed
indm_uniq = unique(indm);
NS_mut_perInd = c(NS_mut_perInd, sum(indm_uniq.mutationType == m2));
Neutral_mut_perInd = c(Neutral_mut_perInd, sum(indm_uniq.mutationType == m1));
genotype = apply(indm_uniq, "sum(indm == applyValue);");
if (isNULL(genotype)) {
next;
}
ID_het = (genotype == 1);
ID_homDer = (genotype == 2);
pos_het = indm_uniq.position[ID_het];
startpos = c(0, pos_het);
endpos = c(pos_het, sim.chromosome.lastPosition);
pos_het_diff = endpos - startpos;
ROH_startpos = startpos[pos_het_diff > ROHcutoff];
ROH_endpos = endpos[pos_het_diff > ROHcutoff];
ROH_length = pos_het_diff[pos_het_diff > ROHcutoff];
ROH_length_sum = sum(ROH_length);
ROH_length_sumPerInd = c(ROH_length_sumPerInd, ROH_length_sum);
NS_mut_in_ROH_perInd = c(NS_mut_in_ROH_perInd, sum(c(apply(indm_uniq.position[ID_homDer & indm_uniq.mutationType == m2], "return(any(applyValue > ROH_startpos & applyValue < ROH_endpos));"), F)));
Neutral_mut_in_ROH_perInd = c(Neutral_mut_in_ROH_perInd, sum(c(apply(indm_uniq.position[ID_homDer & indm_uniq.mutationType == m1], "return(any(applyValue > ROH_startpos & applyValue < ROH_endpos));"), F)));
}
NS_mut_Not_In_ROH_perInd = sum(NS_mut_perInd - NS_mut_in_ROH_perInd);
Neutral_mut_Not_In_ROH_perInd = sum(Neutral_mut_perInd - Neutral_mut_in_ROH_perInd);
cat("# " + sim.generation + " " + p1.individuals.size() + " " + sampleSize + " " + mutLoad + " " + mutLoad_fixed + " " + meanFitness + " " + sum(m_uniq_polym.mutationType.id == 1) + " " + sum(m_uniq_polym.mutationType.id == 2) + " " + numFixedDel + " " + sum(m_uniq_polym.mutationType.id == 1)/(nc_length_total_c + in_length_total_c + ex_length_total_c/(Lns_over_Ls+1)) + " " + sum(m_uniq_polym.mutationType.id == 2)/(ex_length_total_c/(Lns_over_Ls+1)*Lns_over_Ls) + " " + mean(ROH_length_sumPerInd) + " " + sum(Neutral_mut_in_ROH_perInd) + " " + sum(NS_mut_in_ROH_perInd) + " " + Neutral_mut_Not_In_ROH_perInd + " " + NS_mut_Not_In_ROH_perInd + " " + inbreedF + "\n");
}
}