Wright’s Fst is a widely used measure of genetic divergence between populations (Hartl and Clark, 1997). Lewontin and Krakauer (1973) proposed that genetic markers with aberrantly high Fst values (“outliers”) could be inferred to be affected by divergent selection. Recently, outlier analyses have enjoyed a renaissance because of the development of new methods based on coalescent simulation (Beaumont and Nichols, 1996; Beaumont and Balding, 2004). Fst variation is still used to eliminate selected markers from population genetic analyses that require neutrality (Luikart et al., 2003), but it is now of primary interest as a signature of divergent selection that permits detection of genomic regions involved in adaptive divergence (Beaumont, 2005; Storz, 2005).
Significant heterogeneity in marker Fst has been documented between ecologically divergent races (Wilding et al., 2001; Emelianov et al., 2004; Rogers and Bernatchez, 2005; Bonin et al., 2006; Oetjen and Reusch, 2007), with the interpretation that Fst outliers must be linked to loci affecting the phenotypic traits known to distinguish the divergent ecotypes, races, or subspecies. However, outlier analysis alone cannot reveal the cause of deviant Fst values, and the conclusion that Fst outliers must be associ-