Fig. 2

The LD signature around a selective sweep. Assume a population with neutral segregating variation (1). A beneficial mutation occurs (shown as a black allele) in subfigure (2). Since the mutation is beneficial, its frequency will increase in the population. Neutral variants that are linked to the beneficial mutation will hitchhike with it (3). Due to recombination, mutations from a neutral background will get linked with the beneficial mutation (4, 5). Finally, the selective sweep completes (6). The LD pattern that emerges from such a process is the elevated LD on each side of the beneficial mutation and the decreased LD for SNPs that are on different sides of the beneficial mutation