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, Duroc..., We assembled the Sus scrofa reference set from previously published high-resolution SNP genotypes, restricting analysis to genotypes produced with Illumina BeadArray technology (San Diego, California) across multiple commercially available arrays (Illumina PorcineSNP60, Illumina PorcineSNP60 v2, Genomic Profiler for Porcine HD, licensed exclusively to GeneSeek, a Neogen Corporation, Lansing, Michigan; Ramos et al., 2009). We augmented previously published genotypes (detailed in Smyser et al., 2020) with a subset of novel genotypes produced for this study (Appendix S1: Table S1). We restricted our analyses to loci that were available across all datasets (influenced by loci shared across arrays and the extent to which publicly available datasets were filtered by authors prior to publication) and mapped to autosomes (Sscrofa11.1 genome assembly; Warr et al., 2020). In sum, we included 33 breeds and 16 populations of European wild boar, representing a total of 1,421 reference samples (Table..., Files are presented as a PLINK binary file family (*.bed/*.bim/*.fam).  Files can be opened with PLINK (freely available at https://www.cog-genomics.org/plink/) or with many other software platforms., We present data files and computer code necessary to recreate the analyses described in:

\"Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)\" by Timothy J. Smyser, Peter Pfaffelhuber, Rachael M. Giglio, Matthew G. DeSaix, Amy J. Davis, Courtney F. Bowden, Michael A. Tabak, Arianna Manunza, Valentin Adrian Balteanu, Marcel Amills, Laura Iacolina, Pamela Walker, Carl Lessard, and Antoinette J. Piaggio and published in Ecosphere

The files include genotypes for 8,422 Sus scrofa, representing 1,421 reference samples organized into K5 reference groups (mixed-commercial breeds, Duroc, heritage breeds, primitive breeds, and European wild boar), 6,566 wild pigs sampled across the invaded range within the contiguous United States, and 435 domestic pigs sampled from 29 Western breeds that were excluded from the reference set to serve as a test set, with genotypes compiled in a *.bed/*.bim/*.fam (binary PED file) file format. All ...