Current geography masks dynamic history of gene flow during speciation in northern Australian birds

During early stages of speciation, genome divergence is greatly influenced by gene flow. As populations diverge, geography can allow or restrict gene flow in the form of barriers. Current geography, e.g. whether sister species are allopatric or parapatric, is often used to predict the potential for gene flow during the divergence process. We test the validity of this assumption in eight meliphagoid bird species codistributed across four regions. These regions are separated by known biogeographic barriers within and between northern Australia and Papua New Guinea. We find that bird populations across the same barrier have a range of divergence levels and probability of gene flow regardless of range connectivity. Geographic distance and maximum range connectivity over time can better predict divergence and probability of gene flow than whether populations are currently allopatric or parapatric. We also find support for a nonlinear decrease of the probability of gene flow during the divergence process. This implies that although gene flow influences divergence early in speciation, other factors associated with higher divergence restrict gene flow later in speciation. Current geography may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.