Data from: Outlier loci highlight the direction of introgression in oaks

Loci considered to be under selection are generally avoided in attempts to
infer past demographic processes as they do not fit neutral model
assumptions. However, opportunities to better reconstruct some aspects of
past demography might thus be missed. Here we examined genetic
differentiation between two sympatric European oak species with
contrasting ecological dynamics (Quercus robur and Q. petraea) with both
outlier (i.e. loci possibly affected by divergent selection between
species or by hitchhiking effects with genomic regions under selection)
and non-outlier loci. We sampled 855 individuals in six mixed forests in
France and genotyped them with a set of 262 SNPs enriched with markers
showing high interspecific differentiation, resulting in accurate species
delimitation. We identified between 13 and 74 interspecific outlier loci,
depending on the coalescent simulation models and parameters used. Greater
genetic diversity was predicted in Q. petraea (a late successional
species) than in Q. robur (an early successional species) as introgression
should theoretically occur predominantly from the resident species to the
invading species. Remarkably, this prediction was verified with outlier
loci but not with non-outlier loci. We suggest that the lower effective
interspecific gene flow at loci showing high interspecific divergence has
better preserved the signal of past asymmetric introgression towards Q.
petraea caused by the species’ contrasting dynamics. Using markers under
selection to reconstruct past demographic processes could therefore have
broader potential than generally recognized.