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If one population experienced selection at a mutant locus that arose in the ancestral population, a partial sweep represents the kind of selection we are interested in detecting.
This lack of diversity and the high linkage disequilibrium around niDf250 suggest a partial sweep of the haplotype linked to niDf250.
We expect this to create a temporary footprint similar to that of a partial sweep (Pennings and Hermisson 2006a, b; Pritchard et al. 2010; Ralph and Coop 2010).
The contrasting patterns between Tajima's D and HEW in TYR might indicate a partial sweep at this locus in the European (healthy) sample.
However, hard sweeps are not the only way for short-term adaptation and soft sweeps, partial sweep and polygenic adaptation are expected to also play a crucial role (for a review, see Pritchard et al. 2010).
Finally, to complement the above approaches focusing on individual SNP frequencies, we implemented the PHS test (Toomajian et al. 2006) to identify regions with extensive haplotype sharing as might be expected from a recent partial sweep.
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Such tests are sometimes considered most suitable for detecting complete sweeps, in contrast to the partial sweeps detected by LD-based methods, but are also highly effective in detecting partial sweeps (Xue et al. 2009).
With two notable exceptions, we find a modest average effect of partial sweeps on the amount of molecular variation.
We find that soft, partial sweeps have a complicated and variable effect on levels of molecular variation (fig. 7).
This approach has been optimized for nearly fixed selective sweeps, whereas the iHS approach has higher power to detect partial sweeps [ 9].
'Partial sweeps' occur when selection acts on multiple loci that are involved in adaptation, but does not necessarily lead to fixation of beneficial alleles at any of them.
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