9.3 Haplotype-based signatures

When a variant changes in frequency, it doesn’t change alone. The variants on the haplotype surrounding it will be pulled along to high frequency. This phenomenon, called hitchhiking, is similar to the haplotype blocks we observe in GWAS result (and both are caused by linkage between variants).

What do you expect to happen to genetic diversity in the region of a selective sweep?

If one haplotype is sweeping to high AF, we expect that genetic diversity in the region decreases because it’s being replaced by the selected haplotype. This is called a selective sweep because variation is being “swept” out of the region.

This decreased diversity signature fades over time as new mutations arise on the haplotype.

Fig. 3. (A) Selective sweeps reduce genetic diversity. (B)-(D) Summary of common signatures of selection.
Fig. 3. (A) Selective sweeps reduce genetic diversity. (B)-(D) Summary of common signatures of selection.
What can the size of the linked haplotype tell us about its evolutionary history?

Because recombination breaks down haplotypes over time, a longer haplotype implies more recent selection. It can also provide information on the strength of selection – if most occurrences of the haplotype in the population are unbroken, selection was strong enough that it didn’t have time to recombine during the sweep.

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