Molecular evolution of two linked genes, Est-6 and Sod, in Drosophila melanogaster

We have obtained 15 sequences of Est-6 from a natural population of Drosoph ila melanogaster to test whether linkage disequilibrium exists between Est- 6 and the closely linked Sod, and whether natural selection may be involved . An early experiment with allozymes had shown linkage disequilibrium betwe en these two loci, while none Was detected between other gene pairs. The So d sequences for the same 15 haplotypes were obtained previously. The two ge nes exhibit similar levels of nucleotide polymorphism, but the patterns are different. In Est-6, there are nine amino acid replacement polymorphisms, one of which accounts for the S-F allozyme polymorphism. In Sod, there is o nly one replacement polymorphism, which corresponds to the S-F allozyme pol ymorphism. The tl transversion/transition ratio is more than five times lar ger in Sod than in Est-6. At the nucleotide level, the S and F alleles of E st-6 make up two allele families that are quite different from each other., while there is relatively little variation within each of them. There are also two families of alleles in Sod, one consisting of a subset of F allele s, and the other consisting of another subset of F alleles, designed F(A), plus all the S alleles. The Sod F(A) and S alleles are completely or nearly identical in nucleotide sequence. except for the replacement mutation that accounts for the allozyme difference. The two allele families have indepen dent evolutionary histories in the two genes. There are traces of statistic ally significant linkage disequilibrium between the two genes that, we sugg est, may have arisen as a consequence of selection favoring one particular sequence at each locus.