DOI: 10.5061/dryad.v6f1g
title: Data from: Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

description: 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.
description: DG_Boar_Ped88 NW European wild boar SNP genotypes in .ped format for PLINK softwareDG_Boar.pedDG_Boar_MapInfo on the 45720 autosomal SNPs in .map file format corresponding to the genotypes in the DG_Boar.ped file for use in PLINK softwareDG_Boar.mapDG_Pig_Ped120 Pig autosomal SNP genotypes from six breeds common in NW Europe in .ped file format for PLINK softwareDG_Pig.pedDG_Pig_MapInfo on the 45720 autosomal SNPs in .map file format corresponding to DG_Pig.ped for use in PLINK file formatDG_Pig.mapDG_Boar_StruStructure file with 88 wild boar SNP genotypes from NW EuropeDG_Boar.struDG_Pig_StruStructure file with 120 Pig SNP genotypes from NW EuropeDG_Pig.struBoar_infowild boar sample info corresponding to the DG_Boar.ped and DG_Boar.stru genotype filesPig_infoPig sample info corresponding to the DG_Pig.ped and DG_Pig.stru genotypesREADMEShort explanation of file content