Understanding speciation requires determining how inherent barriers to gene flow (reproductive isolation, RI) evolve between populations. The field of population genomics attempts to address this question by characterizing genome-wide patterns of divergence between taxa, often utilizing next-generation sequencing. Here, we focus on a central assumption of such “genome scans”: regions displaying high levels of differentiation contain loci contributing to RI. Three major issues are discussed concerning the relationship between gene flow, genomic divergence, and speciation: () patterns expected in the presence versus absence of gene flow; () processes, such as direct selection and genetic hitchhiking, allowing for divergence with gene flow; and () the consequences of the timing of when gene flow occurs during speciation (e.g., continuous gene flow versus gene flow following secondary contact after a period of initial allopatric divergence). Theory and existing data are presented for each issue, and avenues for future work are highlighted.


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  • Article Type: Review Article
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