<p>In all models, a single population of chromosomes (circles) splits into two nascent species, distinguishable by sets of genetic differences. At each time point, the most frequent multilocus genotype is shown, but other chromosomes could be segregating in the population at lower frequencies. Different haplotypes (or clonal frames) are shown as black or white circles. The ancestral niche is shown in blue and a new niche in orange. Gene flow (recombination) between species is indicated by horizontal connections between branches. (<b>A</b>) In the simplest model of speciation with gene flow, a single mutation controlling sexual isolation (but not under selection) is the only divergent locus (yellow square), with other loci experiencing gene flow between incipient species. (<b>B</b>) Selection during speciation can produce a pattern of genetic diversity across the genome very similar to (A), but species are expected to be longer-lived. Mutations under selection at early and later stages of speciation are shown as orange stars. (<b>C</b>) Allopatric speciation with a population bottleneck and neutral divergence of species. As in (A), competitive exclusion should lead to the extinction of one species if they come back into contact. (<b>D</b>) Without gene flow, the mutation under selection between species (orange star) will purge diversity genome-wide as it sweeps through one population, resulting in genome-wide divergence from the other population.</p
