Geographic Mode of Speciation and Genomic Divergence

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: (a) patterns expected in the presence versus absence of gene flow; (b) processes, such as direct selection and genetic hitchhiking, allowing for divergence with gene flow; and (c) 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.