Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)

The rapid expansion of wild pigs (Sus scrofa) throughout the United States
(US) has been fueled by unlawful introductions, with invasive populations
causing extensive crop losses, damaging native ecosystems, and serving as
a reservoir for disease. Multiple states have passed laws prohibiting the
possession or transport of wild pigs. However, genetic and phenotypic
similarities between domestic pigs and invasive wild pigs – which
overwhelmingly represent domestic pig-wild boar hybrids – pose a challenge
for the enforcement of such regulations. We sought to exploit wild boar
ancestry as a common attribute among the vast majority of invasive wild
pigs as a means of genetically differentiating wild pigs from breeds of
domestic pigs found within the US. We organized reference high-density
single nucleotide polymorphism genotypes (1,039 samples from 33 domestic
breeds and 382 samples from 16 wild boar populations) into five
genetically cohesive reference groups: mixed-commercial breeds, Durocs,
heritage breeds, primitive breeds, and wild boar. Building upon
well-established genetic clustering approaches, we structured the test
statistic to describe the difference in the likelihood of a given
genotype’s ancestry vectors (sensu genetic clustering analysis) if derived
strictly from the four described domestic pig reference groups versus
allowing for admixture from the wild boar group. By fitting statistical
distributions to test statistics of reference domestic pigs, we
characterized the distribution of the null hypothesis – that a given
genotype descends strictly from domestic pig reference groups. We tested
the approach with simulated genotypes and empirical data from an
additional 29 breeds of domestic pig represented by 435 unique genotypes;
all associated test statistics for simulated and empirical domestic pig
challenge sets fell within the distribution of reference domestic pigs. We
then evaluated 6,566 invasive wild pigs sampled across the contiguous
United States, of which 63% exceeded the maximum threshold for domestic
pigs and could be statistically classified as possessing wild boar
ancestry. This approach provides a scientific foundation to enforce
regulations prohibiting the possession of this destructive invasive
species. Further, this computationally efficient and generalizable
approach could be readily adapted to quantify gene flow among ecological
systems of conservation or management concern.