DNA Polymorphism in the ?-Esterase Gene Cluster of Drosophila melanogaster

We have analyzed nucleotide polymorphism within a 5.3-kb region encompassing the functional Est-6 gene and the (psi)Est-6 putative pseudogene in 28 strains of Drosophila melanogaster and one of D. simulans. Two divergent sequence types were detected, which are not perfectly associated with Est-6 allozyme variation. The level of variation (pi) is very close in the 5ʹ-flanking region (0.0059) and Est-6 gene (0.0057), but significantly higher in the intergenic region (0.0141) and putative pseudogene (0.0122). The variation in the 3ʹ-flanking region is intermediate (0.0083). These observations may reflect different levels of purifying selection in the different regions. Strong linkage disequilibrium occurs within the region studied, with the largest values revealed in the putative pseudogene and 3ʹflanking region. Moreover, recombination is restricted within (psi)Est-6. Gene conversion is detected both within and (to a lesser extent) between Est-6 and (psi)Est-6. The data indicate that (psi)Est-6 exhibits some characteristics that are typical of nonfunctional genes, while other characteristics are typically attributed to functional genes; the same situation has been observed in other pseudogenes (including Drosophila). The results of structural entropy analysis demonstrate higher structural ordering in Est-6 than in (psi)Est-6, in accordance with expectations if (psi)Est-6 is indeed a pseudogene. Taking into account that the function of (psi)Est-6 is not known (but could exist) and following the terminology of J. Brosius and S. J. Gould, we suggest that the term "potogene" may be appropriate for (psi)Est-6, indicating that it is a potential gene that may have acquired some distinctive but unknown function.