Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions

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.