1991; Begun and Aquadro, 1992; Martín-Campos et al., 1992; Langley et al., 1993). We therefore reject our strict neutral hypothesis, concluding that regions of low recombination do not have low levels of variation because they have low neutral mutation rates.

Hitchhiking With Favorable Mutations Hypothesis

Another hypothesis that has been proposed to explain the pattern of sequence variation is the hitchhiking or "selective sweeps" model (Maynard Smith and Haigh, 1974; Kaplan et al., 1989; Stephan et al. , 1992; Wiehe and Stephan, 1993). Under this model, the low levels of polymorphism in regions of low recombination are due to the hitchhiking effect of selectively advantageous mutants that sweep through the population and, in the process, eliminate variation at tightly linked sites. In regions of low recombination, large chunks of DNA are swept to fixation by such selection events, whereas in regions of high recombination, only small chunks are swept to fixation. If such selection events are steadily occurring in both high and low recombination regions, the result will be a lower steady-state level of variation in regions of low recombination. If this selective sweeps interpretation is correct, it should be possible to estimate some of the parameters of the population genetic process involved. Indeed, Wiehe and Stephan (1993) have developed a method to estimate an important rate parameter from the patterns of reduced variation. (They assume that most of the variation that is seen is neutral but that the levels of variation are, in some cases, strongly affected by occasional selective sweeps.) The development of this estimation method is quite significant, demonstrating an additional way in which inferences about the mode of molecular evolution can be made from patterns of polymorphism and divergence. Further work is clearly warranted to investigate other properties of this model and to assess the robustness of the rate estimates. Although there remains much to be investigated, this model can account for some important features of the data.

Background Selection Model

Recently, a quite different hypothesis, referred to as the background selection model, has been proposed to account, at least in part, for the low levels of variation in regions of low recombination (Charlesworth et al., 1993). In this model, as with the selective sweeps model, one focuses on the level of neutral variation that will be maintained at a locus embedded in the midst of a large number of other loci at which mutations can occur that are not selectively neutral. Figure 1A illustrates

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