simulate single species with multiple clusters (geographic separation)

[jssd...@gmail.com]

I'm interested in simulating trees for a single species, having clade-like structure (e.g. three separate clusters [three geographic locations], separated by long internal branches), vary the number of individuals in each group, and vary the number of groups. Can SimPhy do this? If so, what is the syntax?

[Diego M.]

I don't fully understand the situation you are describing. Which kind of model would be behind that structure? Are those clades reproductively isolated? You could provide a species tree with the population structure you want and then simulate gene trees along it, but there would not be migration/introgression between them.

I may be able to provide more advice if you give me more specific information on your objective.

Best,

          Diego M.