A | In the top two panel rows, horizontal lines represent haplotypes in a population at a particular genomic locus, with distinct colours representing different genetic backgrounds (compared to well-mixed reference genetic backgrounds indicated in blue). A hard sweep (Aa) involves the fixation of a single new beneficial mutation, whereas a soft sweep (Ab) involves fixation of selectively equivalent alleles that occur at intermediate frequency (i.e. on differing genetic backgrounds) in the population at the onset of selection. Adaptation by polygenic selection (Ac) causes an increase in the frequency of alleles at many loci, but selection does not necessarily drive fixation at any given locus (i.e. multiple partial sweeps). Background selection (Ad) eliminates deleterious mutations and the genetic backgrounds linked to them. Beneficial alleles are represented by circles and stars represent deleterious alleles. The chromosome segment represents a region with a uniform rate of recombination. Dotted lines in the bottom row of panels represent the equilibrium expectation for neutral polymorphism; solid curves show qualitative patterns of neutral polymorphism across the chromosome region. B Differences among species in a broad range of factors could vary the strength of observed signatures of selection at linked sites as caused by recurrent genetic hitchhiking or background selection. Arrows indicate factors associated with recombination (red), selection (blue) and population demography (purple) that tend to exacerbate the effects of linked selection; bars indicate mitigating factors. This diagram is meant as a general summary, as the details of parameter values can change the influence of some exacerbating and mitigating factors.