Selective sweep of a novel advantageous mutation:
Hitchhiking of a linked neutral SNP
A selective "sweep"
of a new SNP in haplotype #6
confers a strong selective advantage and rapidly
replaces the other haplotypes. Ordinarily this would
eliminate the SNP
in those haplotypes. However, if during the sweep,
genetic recombination occurs between haplotypes
##5 & 6, the SNP
in #5 is transposed to a copy of #6,
creating a modified haplotype the combines the red & blue SNPs.
The selective sweep is driven by the selective advantage of the red SNP: the neutral blue SNP is now carried along with the red SNP by linkage, irrespective of selection. This phenomenon is called "hitchhiking", and for a haplotype shown to be subject to positive selection, makes it difficult to determine which of the several linked SNPs is actually responsible. For example, an inherited predisposition to a medical condition in a particular family may be mapped to an area of the short arm of a chromosome. Because the entire region is inherited as a single linkage group, many SNP differences between this region and homologous regions in other unaffected families must be compared.
In such cases, the "candidate gene" approach may be used to narrow the range of SNPs to be examined, by focus on those genes functionally related to the condition of interest.
The selective sweep is driven by the selective advantage of the red SNP: the neutral blue SNP is now carried along with the red SNP by linkage, irrespective of selection. This phenomenon is called "hitchhiking", and for a haplotype shown to be subject to positive selection, makes it difficult to determine which of the several linked SNPs is actually responsible. For example, an inherited predisposition to a medical condition in a particular family may be mapped to an area of the short arm of a chromosome. Because the entire region is inherited as a single linkage group, many SNP differences between this region and homologous regions in other unaffected families must be compared.
In such cases, the "candidate gene" approach may be used to narrow the range of SNPs to be examined, by focus on those genes functionally related to the condition of interest.
Figure modified after © 2013 by Sinauer; Text material © 2025 by Steven M. Carr