Yeast can be engineered to carry human chromosomes; highly diverged ducks can produce viable, fertile offspring; and mitochondrial genes can move between widely divergent groups of plants. Some sunflower or oak species have porous genomes; mice, crickets, birds, and butterflies form hybrid zones; and bacterial lineages have been exchanging genes for several billion years. Even so, nature is discrete and full of species. Here, we discuss some of the ingredients that make nature discrete and can lead to clustering even in the presence of gene flow. Many of these results have been recently published, in this issue and elsewhere, and were discussed at the Genetics of Speciation Symposium held at the annual meeting of the American Genetics Association, Vancouver, Canada, in 2006.