. "Explaining Low Levels of DNA Sequence Variation in Regions of the Drosophila Genome with Low Recombination Rates." Tempo and Mode in Evolution: Genetics and Paleontology 50 Years After Simpson. Washington, DC: The National Academies Press, 1995.
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population genetic processes. Several hypotheses and population genetic models that may account for the data will be discussed. Most of the discussion will concern a "background selection" model that may account for some important aspects of the data.
The data that will be considered here are primarily DNA polymorphism data from a number of loci primarily in Drosophila melanogaster and Drosophila simulans. The salient feature of these data, the focus of this paper, is the following: Regions of the Drosophila genome with low rates of recombination per base pair exhibit low levels of polymorphism within populations (Aguadé et al., 1989; Stephan and Langley, 1989; Berry et al., 1991; Begun and Aquadro, 1992; Martín-Campos et al., 1992; Stephan and Mitchell, 1992; Langley et al., 1993). A summary of these data that display the remarkable correlation between recombination rates and levels of polymorphism is given by Begun and Aquadro (1992) and Aquadro et al., (1994). In the following paragraphs, three hypotheses to account for these data will be described. They are (i) a strictly neutral hypothesis, (ii) a hitchhiking with selective sweeps of advantageous mutations hypothesis, and (iii) a background selection of deleterious mutations hypothesis.
A Strictly Neutral Hypothesis
A very simple though interesting hypothesis to explain the correlation of recombination rates with polymorphism levels is a completely neutral one: Regions of low recombination might have low levels of polymorphism because they have low neutral mutation rates. These low neutral mutation rates in regions of low recombination might result from high average levels of constraint in those parts of the genome or because the spontaneous mutation rates are low there. Either of these possibilities would be interesting and surprising, since there is no a priori reason to suspect that mutation rates are lower or constraints are higher in regions of low recombination. Fortunately, there is a simple and powerful way to test this strict neutral interpretation: Examine the levels of divergence between species in these regions of high and low recombination. Under our neutral interpretation, regions of low recombination ought to have low levels of divergence compared to the levels of divergence in regions of high recombination, because the rate divergence under the neutral model is equal to the neutral mutation rate. The data in this regard are quite clear. Regions of low recombination are not diverging more slowly between species than are regions of high recombination (Berry et al.,