The effect of selected linked locus on heterozygosity of neutral alleles (the hitch-hiking effect)

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Abstract
SUMMARY: A diffusion model was developed to investigate the effect of a mutant substitution by natural selection on heterozygosity at a linked neutral locus. Using this theory, we made extensive numerical analyses to compute the expected total heterozygosity (i.e. the sum of the fraction of heterozygotes over all generations until fixation or loss) at the neutral locus. It was shown that the hitch-hiking effect is generally unimportant as a mechanism for reducing heterozygosity. The effect becomes significant only when the recombination fraction between the selected and the neutral marker loci is smaller than the selection coefficient. In order to check the validity of the mathematical theory, Monte Carlo experiments were performed, and the results were in agreement. It has been suggested that linkage is important only in transient small populations such as at the time of speciation.