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FIGURE 1-5 Two views of how to delineate regions of divergence hitchhiking. (A) A single region of divergence hitchhiking around QTL affecting one or more traits (indicated by differently shaded squares) is defined by a cluster of Fst outliers. (B) Each outlier defines a a separate hitchhiking region, bounded by a low Fst marker. In this view, outliers are thought to be either under direct divergent selection, or tightly linked to a selected gene.

FIGURE 1-5 Two views of how to delineate regions of divergence hitchhiking. (A) A single region of divergence hitchhiking around QTL affecting one or more traits (indicated by differently shaded squares) is defined by a cluster of Fst outliers. (B) Each outlier defines a a separate hitchhiking region, bounded by a low Fst marker. In this view, outliers are thought to be either under direct divergent selection, or tightly linked to a selected gene.

II.
Each Outlier Corresponds to a Gene or QTL Under Selection or Is Itself Under Selection (Fig. 1.5B).

Ting et al. (2000) found that a DNA sequence just 1,100 bp away from the hybrid sterility gene Odysseus (Ody) was not divergent between the 2 parental species, and from this single observation they concluded that the hitchhiking region around Ody must be extremely small. Wood et al. (2008) and Smadja et al. (2008) extend this idea by suggesting that the nearest genomic region of low genetic divergence to an Fst outlier marks the boundary of its hitchhiking region (Fig. 1.5B).

Several observations are inconsistent with this hypothesis. First, outliers are easy to find. Even in studies with just a few markers (Wilding et al., 2001; Emelianov et al., 2004; Rogers and Bernatchez, 2007; Via and West, 2008), 5% or more of tested markers are generally Fst outliers. Taking 5% as a minimal estimate, this observation implies either that hitchhiking



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