Fig. 2

The initial population consists of white-eyed flies that carry two alleles at the Near marker (green or blue), two alleles at the Far marker (purpleor yellow), and white eye allele at the eye color gene. A red-eyed fly is introduced that carries the blue allele at Near, yellow at Far, and red at the eye color gene. The red eye allele is advantageous and sweeps to high frequency in the population. The blue allele at Near is located close to the advantageous eye color and hitchhikes with the red eye color. The Far allele is located 22 million base pairs down at the other end of the chromosome. Recombination breaks down linkage between eye color and Far, so both yellow and purple alleles persist