Surprisingly, the spatial distribution of the mapped Fst outliers suggests that the signature left by divergent phenotypic selection on neutral markers can extend far from major QTL: the average outlier was 10.6 cM from the nearest QTL. A similar result was found for traits involved in the divergence of whitefish morphs in postglacial lakes (Rogers and Bernatchez, 2007), where the average outlier was 16.2 cM from the nearest QTL. In both systems, the hitchhiking regions around divergently selected QTL are far larger than expected. After a selective sweep through a large panmictic population, linkage disequilibrium rapidly erodes except in areas of reduced recombination (Begun and Aquadro, 1992). Although reduced recombination is, in fact, the explanation for the large hitchhiking regions we observed, they arise not from suppression of recombination per se, but from a reduction in the “effective recombination” between locally adapted QTL alleles in divergent populations that are subdivided (i.e., no longer randomly mating).
Charlesworth et al. (1997) analyzed the potential for hitchhiking when populations are subdivided by divergent (local) selection. Using a simulation analysis, they found that regions of linkage disequilibrium of the size we observed (Via and West, 2008) can be maintained around a divergently selected locus. This unexpected result occurs because subdivision reduces the opportunity for recombination between locally adapted QTL