Data from: Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

Present-day genetic introgression from domestic pigs into European wild
boar has been suggested in various studies. However, no hybrids have been
identified beyond doubt mainly because available methods were unable to
quantify the extent of introgression and rule out natural processes.
Genetic introgression from domestic pigs may have far-reaching ecological
consequences by altering traits like the reproduction rate or immunology
of wild boar. In this study, we demonstrate a novel approach to
investigate genetic introgression in a Northwest (NW) European wild boar
data set using a genome-wide single nucleotide polymorphism (SNP) assay
developed for domestic pigs. We quantified the extent of introgression
using allele frequency spectrum analysis, in silico hybridization
simulations and genome distribution patterns of introgressed SNPs. Levels
of recent introgression in the study area were expected to be low, as pig
farming practices are prevailingly intensive and indoors. However,
evidence was found for geographically widespread presence of domestic pig
SNPs in 10% of analysed wild boar. This was supported by the
identification of two different pig mitochondrial DNA haplotypes in three
of the identified hybrid wild boar, suggesting that introgression had
occurred from multiple sources (pig breeds). In silico hybridization
simulations showed that the level of introgression in the identified
hybrid wild boar is equivalent to first-generation hybrids until
fifth-generation backcrosses with wild boar. The distribution pattern of
introgressed SNPs supported these assignments in four of nine hybrids. The
other five hybrids are considered advanced-generation hybrids, resulting
from interbreeding among hybrid individuals. Three of nine hybrids were
genetically associated with a different wild boar population than the one
in which they were sampled. This discrepancy suggests that genetic
introgression has occurred through the escape or release of an already
hybridized farmed wild boar stock. We conclude that genetic introgression
from domestic pigs into NW European wild boar populations is more recent
and more common than expected and that genome-wide SNP analysis is a
promising tool to quantify recent hybridization in free-living
populations.