Using estimates of sequence divergence, several taxa have been found to have sharply increased molecular evolutionary rates between the most recently diverged species studied (reviewed in Peterson and Masel, 2009). This ‘acceleration of the molecular clock at short timescales’ has been considered puzzling, and has been attributed to changes in mutation rates. However, it has also been suggested that this is only an apparent acceleration caused by the segregation of lineages present in the ancestral population of recently diverged species. The common ancestor of two alleles at a locus existed before two species became isolated, and so divergence times between alleles in two species exceed the species divergence times (Gillespie and Langley, 1979), which ‘would exaggerate the genetic difference between the populations’ (Nei, 1971). For recently diverged species, this can add substantially to the numbers of sites with sequence differences (Figure 1a). Peterson and Masel have now studied this possibility thoroughly, and show that this effect can explain the observations.