Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome.
As first noted by Kojima and Schaeffer (1967) and Maynard Smith and Haigh (1974), the dynamics of a neutral allele are strongly influenced by selection at a linked locus. Over fifty years later, we are still trying to fully understand all of the ramifications of this idea. Chapter 3 provided a brief introduction to two rather different scenarios involving linkage to a selected locus: selective sweeps and background selection. In this chapter we further unpack these concepts, presenting a much richer theoretical treatment and a more detailed account of some of their potential consequences. Results presented here underpin many of the tests for detecting currently ongoing, or very recent, selection developed in Chapter 9. Our treatment is structured as follows. We start with a review of the basic terminology for different scenarios all loosely referred to as sweeps. Next, we review the populationgenetics of hard sweeps, detailing how neutral variation is perturbed by positive selection at linked sites. We then turn to soft sweeps, wherein a preexisting allele is suddenly placed under selection, generating a different pattern of background neutral variation relative to a hard sweep. This naturally leads to a discussion as to whether adaptation to a new challenge occurs by existing variation or by waiting for a new favorable mutation, as well as to the notion of a polygenic sweep (small allele-frequency changes at a number of loci). We conclude with a discussion of the implications of repeated bouts of selection at linked sites (be they recurrent sweeps or background selection) for substitution rates at linked sites, codon usage bias, and whether the current data suggests that a paradigm shift away from Kimura’s (1983) classical neutral theory of molecular evolution is needed.