Dear Miguel & Eduardo.
This is correct, except that you should keep in mind that pbtree (like
most, but not all, such simulators) generates trees from the first
speciation event. Thus, the correct procedure must first involve drawing
a wait time from an exponential distribution, deciding if
Maybe you could use a birth-death model. You can estimate the speciation
rate and extinction rate from your original tree, and use those parameters
to run simulations of trees for 5 My with the pbtree function from
phytools. Run as many simulations as you have living tips in your original
tree,
