Figure 1. Alternative modes of divergence.

All models assume that an ancestral population of size N_A splits into two populations at time t_s (time of split). The two present day populations have effective sizes N₁ and N₂, respectively. In model A) the migration rate is zero in both directions, which corresponds to an allopatric divergence scenario. B–D) Alternative models in which populations have been exchanging migrants. B) Gene flow at constant rates since the split from the ancestral population. Migration rates are assumed constant through time but gene flow can be asymmetric, i.e. one migration rate for each direction. C) Scenario in which populations begin diverging in the presence of gene flow but experience a cessation of gene flow after some time t_i (time since isolation). If the lack of current gene flow in this model is due to reproductive isolation then this represents a history in which divergence occurred to the point of speciation in the presence of gene flow. In D) we consider the alternative migration history where populations were isolated and diverged for a period of time in the absence of gene flow, followed by secondary contact at t_sc (time of secondary contact), and the introgression of alleles from the other population by gene flow.