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 chromosome (Ost and O3+4) and in the Acph-1 electrophoretic allele (Acph-1100, Acph-1054, and Acph-1>100). The ACPH-1 protein exhibits much more variation than previously detected by electrophoresis. The amino acid replacements responsible for the Acph-1054 and Acph-1>100 electrophoretic variants are different within Ost and within O3+4, which invalidates all previous studies on linkage disequilibrium between chromosomal and allozyme polymorphisms at this locus. The Acph-1>100 allele within O3+4 has a recent origin, while both Acph-1054 alleles are rather old. Levels of nucleotide variation are higher within the O3+4 than within the Ost arrangement except for nonsynonymous sites. The McDonald and Kreitman test shows a significant excess of nonsynonymous polymorphisms within Ost when D. guanche is used as the outgroup. According to the nearly neutral model of molecular evolution, this excess is consistent with a smaller effective size of Ost relative to O3+4 arrangements. A smaller population size, a lower recombination, and a more recent bottleneck might be contributing to the smaller effective size of Ost.