polytomy and ancestral gene flow

[gargkritika]

Dear Dr. Gronau,

I would like to know if I can model Polytomy in G-PhoCS. Also please let me know if it is possible to model gene flow to an ancestor of two daughter lineages.

Thank you very much.

Best regards,
Kritika

[igronau]

You may model gene flow into / from an ancestral population by introducing the appropriate migration band. Note that if you do this, it constrains the divergence times, since if you have a migration band from population A to population B, then their "life spans" must intersect. So you should make sure that if A or B are ancestral populations, then their times likely intersect with the other population (if they're both sampled populations, then this is guarateed).

There is no direct way to model polytomy, but you have polytomy between populations A, B, and C, then you can specify an arbitrary topology for these three population, and you'll indeed see if the two divergence times end up being estimated close to each other. You may also try all three alternative topologies to make sure.