Kreitman and Aguadé

A few years after Kreitman [2] appeared, Kreitman and Aguadé [3] published an analysis in which they looked at levels of nucleotide diversity in the Adh region, as revealed through analysis of RFLPs, in D. melanogaster and the closely related D. simulans. Why the comparative approach? Well, Kreitman and Aguadé recognized that the neutral theory of molecular evolution makes two predictions that are related to the underlying mutation rate:

• If mutations are neutral, the substitution rate is equal to the mutation rate.

• If mutations are neutral, the diversity within populations should be about $4N_e\mu/(4N_e\mu + 1)$.

Thus, if variation at the Adh locus in D. melanogaster is selectively neutral, the amount of divergence between D. melanogaster and D. simulans should be related to the amount of diversity within each. What they found instead is summarized in Table 1.

Table 1: Diversity and divergence in the Adh region of Drosophila (from [3]).

	5' flanking	Adh locus	3' flanking
Diversity$^1$
Observed	9	14	2
Expected	10.8	10.8	3.4
Divergence$^2$
Observed	86	48	31
Expected	55	76.9	33.1
$^1$Number of polymorphic sites within D. melanogaster
$^2$Number of nucleotide differences between D. melanogaster and D. simulans

Notice that there is substantially less divergence at the Adh locus than would be expected, based on the average level of divergence across the entire region. That's consistent with the earlier observation that most amino acid substitutions are selected against. On the other hand, there is more nucleotide diversity within D. melanogaster than would be expected based on the levels of diversity seen in across the entire region. What gives?

Time for a trip down memory lane. Remember something called ``coalescent theory?'' It told us that for a sample of neutral genes from a population, the expected time back to a common ancestor for all of them is about $4N_e$ for a nuclear gene in a diploid population. That means there's been about $4N_e$ generations for mutations to occur. Suppose, however, that the electrophoretic polymorphism were being maintained by natural selection. Then we might well expect that it would be maintained for a lot longer than $4N_e$ generations. If so, there would be a lot more time for diversity to accumulate. Thus, the excess diversity could be accounted for if there is balancing selection at ADH.