a marker 10.6 cM from a QTL is the original recombination probability (0.106) discounted by the probability that a migrant will choose the alternate habitat and survive there (0.11 × 0.17), and the relative fecundity of F1 hybrids (0.5), making the effective recombination rate for that marker (0.106) × (0.11) × (0.17) × (0.5) = 0.001.
This calculation suggests that the average outlier, at a nominal distance of 10.6 cM from the nearest QTL on the linkage map (Via and West, 2008), has an effective map distance to that QTL of only ≈0.1 cM. In these populations, even a marker 50 cM from a divergently selected QTL has an effective map distance of only 0.5 cM as a result of the large decrease in effective migration caused by extensive ecologically based reproductive isolation. This estimated difference between nominal recombination and effective recombination between subdivided populations shows why such a large genomic region is expected to remain in linkage disequilibrium with a QTL under divergent selection during ecological speciation with gene flow.
It is of interest that the magnitude of effective recombination in a given genomic region changes over time as ecological specialization evolves, because greater specialization increases the magnitude of resource-based selection against migrants and hybrids. This can be illustrated with a simple example. Imagine that early in divergence only a few QTL have differentiated such that extent of habitat choice and the disadvantage of migrants or F1 is only 25% as strong as at present. Then, only 22% of potential migrants would refuse the alternate host (78% accept), selection against a migrant would be s = 0.21 (relative fitness of migrants = 0.79), and the relative fecundity of an F1 hybrid would be 0.875, making the effective rate of recombination of the average outlier with the nearest QTL (0.106) × (0.78) × (0.79) × (0.875) = 0.057. Thus, at this earlier point in divergence, the average outlier would have an effective map distance of 5.7 cM from the nearest QTL. Although smaller than the nominal map distance of 10.6 cM, it is far from the tight effective linkage seen at present. The size of each region of divergence hitchhiking therefore depends not only on the strength of divergent selection directly on that genomic region, but also on the extent to which effective migration is reduced by the earlier divergence of other QTL alleles throughout the genome.
Divergence hitchhiking has the same general effect on interrace recombination and speciation as a chromosomal inversion that happens to contain 1 or more key QTL [e.g., Noor et al. (2001), Rieseberg (2001), Machado et al. (2007)]. However, unlike inversions, which must occur relatively infrequently at the site of key QTL, divergence hitchhiking appears automatically around any QTL under strong divergent selection. More-