Figure 8.23 Plots of nucleotide diversity within D. melanogaster populations (a) and divergence between D. melanogaster and D. simulans (b) by the coefficient of exchange, a measure of the recombination rate, for numerous loci. The nucleotide diversity at a locus decreases along with the recombination rate (a). The correlation of polymorphism and the recombination rate at a locus could be explained by neutral theory if loci with lower recombination rates also happen to have lower mutation rates. Under this neutral hypothesis, divergence rates would also be correlated with recombination rates since both polymorphism and divergence increase as the mutation rate increases. An alternative explanation for the correlation of recombination and polymorphism is the action of natural selection on beneficial mutations that has caused hitch-hiking and a reduction of polymorphism due to selective sweeps. Divergence rates at a subset of the loci (b) suggest that divergence and recombination rates are independent, rejecting the neutral hypothesis for these data. Data from Begun and Aquadro (1992).

polymorphism and recombination rate in Drosophila are shown in Fig. 8.23. While polymorphism in D. melanogaster clearly increases with the recombination rate, levels of divergence between D. melanogaster and D. simulans for a subset of the same loci are independent of the recombination rate. These data therefore reject the neutral hypothesis. An alternative explanation for these data is the operation of natural selection on beneficial mutations that has resulted in selective sweeps. The strength of genetic hitch-hiking and the amount of polymorphism lost to selective sweeps decreases with increasing recombination because recombination reduces gametic disequilibrium between a selected mutation and neighboring sites. However, selective sweeps have no impact on

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