Rev Language Reference


dnDuplicationLoss - Multispecies coalescent Distribution

Multispecies coalescent distribution describing how gene trees can be generated from within a species tree given a constant effective population size. Requires an ultrametric species tree, a single effective population size (a single real positive), and taxa with species and individual names.

Usage

dnDuplicationLoss(TimeTree individualTree, RealPos lambda, RealPos mu, Taxon[] taxa)

Arguments

individualTree : TimeTree (pass by const reference)
The individual tree in which the gene trees evolve.
lambda : RealPos (pass by const reference)
The duplication rate(s).
mu : RealPos (pass by const reference)
The loss rate(s).
taxa : Taxon[] (pass by value)
The vector of taxa which have species and individual names.

Domain Type

Details

The species tree must be ultrametric. The effective population size is constant across the species tree.

Example

# We are going to save the trees we simulate in the folder simulatedTrees:
dataFolder = "simulatedTrees/" 
# Let’s simulate a species tree with 10 taxa, 2 gene trees, 3 alleles per species:
n_species <- 10
n_genes <- 2
n_alleles <- 3
# we simulate an ultrametric species tree:
# Species names:
for (i in 1:n_species) {
        species[i] <- taxon(taxonName="Species_"+i, speciesName="Species_"+i)
}
spTree ~ dnBirthDeath(lambda=0.3, mu=0.2, rootAge=10, rho=1, samplingStrategy="uniform", condition="nTaxa", taxa=species)
print(spTree)
# let's pick a constant effective population size of 50:
popSize <- 50
# let's simulate gene trees now:
# taxa names:
for (g in 1:n_genes) {
  for (i in 1:n_species) {
    for (j in 1:n_alleles) {
        taxons[g][(i-1)*n_alleles+j] <- taxon(taxonName="Species_"+i+"_"+j, speciesName="Species_"+i)
    }
  }
  geneTrees[g] ~ dnMultiSpeciesCoalescent(speciesTree=spTree, Ne=popSize, taxa=taxons[g])
  print(geneTrees[g])
}
# We can save the species tree and the gene trees: 
write(spTree, filename=dataFolder+"speciesTree")
# Saving the gene trees
for (i in 1:(n_genes)) {
  write(geneTrees[i], filename=dataFolder+"geneTree_"+i+".tree")
}

See Also