At this point, we've refined the neutral theory quite a bit. Our understanding of how molecules evolve now recognizes that some substitutions are more likely than others, but we're still proceeding under the assumption that most nucleotide substitutions are neutral or detrimental. So far we've argued that variation like what Hubby and Lewontin [1,5] found is not likely to be maintained by natural selection. But we have strong evidence that heterozygotes for the sickle-cell allele are more fit than either homozygote in human populations where malaria is prevalent. That's an example where selection is acting to maintain a polymorphism, not to eliminate it. Are there other examples? How could we detect them?
In the 1970s a variety of studies suggested that a polymorphism in the locus coding for alcohol dehydrogenase in Drosophila melanogaster might not only be subject to selection but that selection may be acting to maintain the polymorphism. As DNA sequencing became more practical at about the same time,1 population geneticists began to realize that comparative analyses of DNA sequences at protein-coding loci could provide a powerful tool for unraveling the action of natural selection. Synonymous sites within a protein-coding sequence provide a powerful standard of comparision. Regardless of
the synonymous positions within the sequence provide an internal control on the amount and pattern of differentiation that should be expected when substitutions.2Thus, if we see different patterns of nucleotide substitution at synonymous and non-synonymous sites, we can infer that selection is having an effect on amino acid substitutions.