In!ersion polymorphisms and nucleotide !ariability in Drosophila

Population genetic models of molecular variation usually assume that most genetic variability is neutral or nearly so (Kimura, 1983). However, even if most variability is neutral, patterns of polymorphism may be indirectly shaped by natural selection (Gillespie, 1997). Indeed, theoretical studies show that neutral variability linked to selected sites may be influenced by different types of natural selection, including balancing selection (Strobeck, 1983; Hudson & Kaplan, 1988), Hill-Robertson interference (Hill & Robertson, 1966) or directional selection (Maynard Smith & Haigh, 1974; Charlesworth et al., 1993; Gillespie, 1997). In all these models of evolution, the recombination rate is a key parameter. Other factors being equal, the lower the recombination rate, the larger the chromosomal segment affected by selection at a linked site. The theoretical importance of recombination is confirmed by what is perhaps one of the most convincing patterns to emerge from population genetics over the last decade: levels of nucleotide polymorphism are reduced in genomic regions with low rates of meiotic crossing-over. Evidence for this trend has been gathered in a wide variety of organisms (Nachman, 1997; Dvorak et al., 1998; Stephan & Langley, 1998; Przeworski et al., 2000). To date, the main body of data comes from Drosophila melanogaster, where the local recombination rate accounts for a large portion of the variance in nucleotide diversity among genes (Aquadro et al., 1994). This general pattern is thought to reflect the distinct effects of variation-reducing selection on neutral variability in different recombination environments. Recombination rates vary both across the genome and between closely related species of Drosophila (cf.