Data from: Detecting the footprints of divergent selection in oaks with linked markers

Genome scans are increasingly used to study ecological speciation,
providing a useful genome-wide perspective on divergent selection in the
presence of gene flow. Here, we compare current approaches to detect
footprints of divergent selection in closely related species. We analyzed
192 individuals from two interfertile European temperate oak species using
30 genomic microsatellites from eight linkage groups. These markers
present little intraspecific differentiation and can be used in
combination to assign individual genotypes to species. We first show that
different outlier detection tests give somewhat different results,
possibly due to model constraints. Second, using linkage information for
these markers, we further characterize the signature of divergent
selection in the presence of gene flow. In particular, we show that
recombination estimates for regions with outlier markers are lower than
those for a control region, in line with a prediction from ecological
speciation theory. Most importantly, we show that analyses at the
haplotype level can distinguish between truly divergent (bi-directional)
selection and positive selection in one of the two species, offering a new
and improved method for characterizing the speciation process.