SNP data in the detection of hybridization levels between wild boar and domestic pig in Europe

Introgression of domestic genes into wild populations is considered to be a threat to biodiversity leading to loss of local adaptation and spread of human selected gene variants. Additionally, the contact between wild and domestic stocks can result in the transmission of infectious diseases. Thus, a better understanding of hybridization patterns in Europe might have important implications for conservation and management of both wild populations and local breeds, as well as for the contingency of infectious diseases.
Here we present the results for the analysis of 235 wild boars (WB; from 22 areas) and 149 domestic pigs (DP; 49 from 5 commercial lines and 100 from 9 local breeds) with the Porcine SNP60 Beadchip.
Principal component analysis shows a clear separation between domestic and wild populations. The network analysis concordantly identifies two main clusters (corresponding to WB and DP) but, additionally, highlights the presence of several individuals, of both ancestries, with intermediate positions. This result was confirmed by Admixture analysis that detected the presence of hybrid individuals in both WB and local domestic pig breeds.
The introgression level varies considerably among populations, from non-detectable to very high. This result might be due to breeding practices, population history and WB management, but it arises questions on domestication and selective processes as well. Additional analyses to identify the presence of human or natural selected regions will be needed to disentangle the observed results.