Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir’s  0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlighted the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

A subset of 12 Corsican wild boars and seven domestic pigs from the Nustrale breed, as well as 14 wild boars from Luxembourg, were genotyped using the Porcine SNP60 v2 BeadChip (Illumina Inc.) following manufacturer’s instructions. GenomeStudio 2.0 software (Illumina Inc.) was employed to call genotypes using a custom cluster file to improve call rates. Only autosomal SNPs, mapping to chromosomes 1 to 18 on the reference genome Sscrofa build 11.1, were retained for analysis. The resulting 60K genotypes were merged with publicly available data from 44 domestic pigs and 60 wild boars sampled in France, Iberia, Italy and Sardinia (Iacolina et al., 2016). Genotypes from 11 Bornean bearded pigs (S. barbatus; Yang et al., 2017) were included in analyses requiring an outgroup (i.e. TREEMIX, see below).

Five SNP data files are provided:

LD-pruned and unpruned PLINK files (.ped and .map) and the TREEMIX infile with S. barbatus outgroup.