Dear all,

I resequenced 3 bird species of the same genera, species A, B and C, there was recent gene flow between A and B.

The mean Fst between A and B was 0.05, and 0.6 between A and C or B and C.

So, I predict that species A and B were very recently diverged compared to species C.

Then I used MCMCtree in PAML to estimate their divergence time based on clock-like CDs sequences, I got about 3 million years divergence time beteen C and (A/B), but 1.5 miliion years divergence time between A and B.

I think this was contradicted by the Fst estimation, because intuitively, the divergence time between A and B should much smaller than 1.5 million years.

MCMCtree calculation was based on only 1 individual, would this bias MCMCtree?

I am still confused about Fst values and divergence time in my focal species, any comments would help a lot!

Best of my wishes,

Dezhi