sweeps at linked loci

Hartfield M & Otto SP 2011 Recombination and hitchhiking of deleterious alleles. Evolution, in press.
doi:10.1111/j.1558-5646.2011.01311.x

  • once established, the frequency of A1B1 can be modeled by the standard deterministic equation for haploid selection
  • p(t) = p0(1 + snet)t / [p0(1 + snet)t + 1 − p0] ... (1)
  • among those alleles that succeed in fixing, the trajectory of the A1B1 haplotype is slightly faster, on average, than given by equation (1)
  • this initial acceleration is taken into account in the diffusion model developed below
  • it turns out to have little effect
  • because rare recombination events that break apart the A1B1 haplotype are most likely to occur when the A1B1 haplotype is intermediate in frequency and not when it initially occurs
  • comparison to the case of a linked neutral allele
  • the dynamics of neutral loci are likely to be affected by the spread nearby of a beneficial allele whenever r is approximately less than sa
  • this rule cannot be used to compare to equation (13) directly
  • our criteria for being "affected" is now quite strict
  • the linked B1 allele must fix due to the sweep
  • if they remain associated, deleterious alleles can hitchhike to fixation as an advantageous allele sweeps through the population
  • Williamson et al. (2007) found possible evidence of such hitchhiking causing the high prevalence of the hereditary hemochromatosis mutation C282Y, due to a selective sweep occurring 150 kb away from the HFE gene where the deleterious C282Y allele is located
  • the hitchhiking of tightly linked deleterious alleles reduces the region in which the sweep is likely to fix surrounding sites
  • (compare eq. 15 to eq. 13)
  • it implies that deleterious hitchhiking can alter experimental estimates of the strength of such sweeps
  • a potential example of these effects was reported by Clegg et al. (1980), who found that linkage disequilibrium in D. melanogaster broke down more quickly than expected (geometric decay at a ratio 1 − r), based on the surrounding markers being neutral and on measured recombination rates between the selected and neutral markers
  • this observation could be explained by recombination untangling advantageous alleles from deleterious backgrounds