Making sense of genomic islands of differentiation in light of speciation

The genomic landscape of differentiation between diverging lineages is often heterogeneous, with 'islands' of elevated differentiation previously interpreted as 'speciation islands' under a model of speciation with gene flow.Alternative processes can generate heterogeneous differentiation landscapes; notable processes include linked selection, variable recombination rates and/or density of targets of selection.Genome scans for regions of elevated differentiation should be based on whole-genome re-sequencing of individually tagged samples with reads mapped to a reference genome assembly.When designing speciation genomic studies, attention should be paid to the possibility of sampling across the speciation continuum and from replicate population pairs, and to the demography of the studied population, including potential gene flow.Analyses of sequence data in speciation genomic studies should incorporate a suite of summary statistics.The field is likely to move forward as a result of an increased use of long-read sequencing technology, the identification of structural variation, the inclusion of recombination rate data and, ultimately, functional studies.