Check out our recent opinion piece in Science where we argue that speciation often involves genetic differentiation at many loci (genes) across the genome. This likely occurs because the effects of natural selection can be coupled across statistically correlated genes, such that selection on one locus spills over to other correlated loci. Thus, one key to understanding the speciation process is understanding the processes by which genes and traits become coupled and cause a transition from polymorphism within a population to geographic variation to genome-wide differentiation and distinct species.