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As is true of virtually every realm of the biological sciences, our understanding of speciation is increasingly informed by the genomic revolution of the past decade. Investigators can ask detailed questions relating to both the extrinsic (e.g. interand intra-population and ecological interactions) and intrinsic (e.g. genome content and architecture) forces that drive speciation. Technologies ranging from restriction-site associated DNA sequencing (RADseq), to whole genome sequencing and assembly, to transcriptomics, to CRISPR are revolutionizing the means by which investigators can both frame and test hypotheses of lineage diversification. Our review aims to examine both extrinsic and intrinsic aspects of speciation. Genome-scale data have already served to fundamentally clarify the role of gene flow during (and after) speciation, although we predict that the differential propensity for speciation among phylogenetic lineages will be one of the most exciting frontiers for future genomic investigation. We propose that a unified theory of speciation will take into account the idiosyncratic features of genomic architecture examined in the light of each organism’s biology and ecology drawn from across the full breadth of the Tree of Life.

What is Speciation Genomics? The roles of ecology, gene flow, and genomic architecture in the formation of species