soft sweep

Zöllner S 2008 Population history and linkage disequilibrium. Encyclopedia Life Sci a0005428.

• the selected allele will be in LD over long distances
• a fact exploited by the extended haplotype homozygosity (EHH) test for selection
• if an allele only came under selection after segregating in the population for many generations (selection on standing variation), the selected allele likely exists on several haplotype backgrounds
• when the selected allele increases in frequency, all those haplotype backgrounds increase in frequency as well
• we do not expect patterns of LD much different from a neutral locus