The relationship between allozyme and chromosomal polymorphism inferred from nucleotide variation at the Acph-1 gene region of Drosophila subobscura

The Acph-1 gene region was sequenced in 51 lines of Drosophila subobscura. Lines differ in their chromosomal arrangement for segment I of the O chromo some (O-st and O3+4) and in the Acph-1 electrophoretic allele (Acph-1(100), Acph-1(054), and Acph-1(>100)). The ACPH-1 protein exhibits much more vari ation than previously detected by electrophoresis. The amino acid replaceme nts responsible for the Acph-1(054) and Acph-1(>100) electrophoretic varian ts are different within O-st and within O3+4, which invalidates all previou s studies on linkage disequilibrium between chromosomal and allozyme polymo rphisms at this locus. The Acph-1(>100) allele within O3+4 has a recent ori gin, while both Acph-1(054) alleles are rather old. Levels of nucleotide va riation are higher within the O3+4 than within the O-st arrangement except for nonsynonymous sites. The McDonald and Kreitman test shows a significant excess of nonsynonymous polymorphisms within O-st when D. guanche is used as the outgroup. According to the nearly neutral model of molecular evoluti on, this excess is consistent with a smaller effective size of O-st relativ e to O3+4 arrangements. A smaller population size, a lower recombination, a nd a more recent bottleneck might be contributing to the smaller effective size of O-st.