In asexual eukaryotes, the two allelic gene copies at a locus are expected to become highly divergent as a result of the independent accumulation of mutations in the absence of segregation. If sexual reproduction was abandoned millions of generations ago, intra-individual allelic divergences can be significantly larger than in species that reproduce sexually. Owing to the disputed existence of truly ancient asexual species, this so-called ‘Meselson effect’ has been put forward as a means of confirming the complete loss of sexual reproduction. Very few attempts have, however, been made at quantifying the effect of sexual reproduction on the degree of divergence between gene copies in an asexual population. Here, I describe how asexual reproduction can be regarded as a special case of population subdivision. Using a slightly modified version of the standard two-deme structured coalescent, I derive the expected coalescence time for a pair of gene copies in an asexual population and show that the Meselson effect is compatible with low rates of sexual reproduction.