Data from: Background selection and FST: consequences for detecting local adaptation

Background selection is a process whereby recurrent deleterious mutations
cause a decrease in the effective population size and genetic diversity at
linked loci. Several authors have suggested that variation in the
intensity of background selection could cause variation in FST across the
genome, which could confound signals of local adaptation in genome scans.
We performed realistic simulations of DNA sequences, using recombination
maps from humans and sticklebacks, to investigate how variation in the
intensity of background selection affects FST and other statistics of
population differentiation in sexual, outcrossing species. We show that,
in populations connected by gene flow, Weir & Cockerham's
(1984) estimator of FST is largely insensitive to locus-to-locus variation
in the intensity of background selection. Unlike FST, however, dXY is
negatively correlated with background selection. Moreover, background
selection does not greatly affect the false positive rate in FST outlier
studies in populations connected by gene flow. Overall, our study
indicates that background selection will not greatly interfere with
finding the variants responsible for local adaptation.