DOI: 10.5061/dryad.b2rbnzsq9
title: Feral swine genotypes and metadata used for identifying translocations in the United States

description: Globalization has led to the frequent movement of species out of their
 native habitat. Some of these species become highly invasive and capable
 of profoundly altering invaded ecosystems. Feral swine (Sus scrofa ×
 domesticus) are recognized as being among the most destructive invasive
 species, with populations established on all continents except Antarctica.
 Within the United States (US), feral swine are responsible for extensive
 crop damage, the destruction of native ecosystems, and the spread of
 disease. Purposeful human-mediated movement of feral swine has contributed
 to their rapid range expansion over the past 30 years. Patterns of
 deliberate introduction of feral swine have not been well described as
 populations may be established or augmented through small, undocumented
 releases. By leveraging an extensive genomic database of 18,789 samples
 genotyped at 35,141 single nucleotide polymorphisms (SNPs), we used deep
 neural networks to identify translocated feral swine across the contiguous
 US. We classified 20% (3,364/16,774) of sampled animals as having been
 translocated and described general patterns of translocation using
 measures of centrality in a network analysis. These findings unveil
 extensive movement of feral swine well beyond their dispersal
 capabilities, including individuals with predicted origins &gt;1,000
 km away from their sampling locations. Our study provides insight into the
 patterns of human-mediated movement of feral swine across the US and from
 Canada to the northern areas of the US. Further, our study validates the
 use of neural networks to study the spread of invasive species.
description: Biological samples (<em>n</em> = 18,789) were
 collected from feral swine throughout their invaded range within the US as
 an extension of damage management and disease surveillance efforts led by
 the USDA along with cooperative agencies. Overwhelmingly, samples were
 collected by USDA‐Animal and Plant Health Inspection Service-Wildlife
 Services personnel. Feral swine were lethally removed through trapping or
 targeted sharpshooting from 2001-2022 as an extension of control efforts
 to reduce threats to agriculture, natural resources, property, and the
 health of humans and livestock. To identify potential translocations from
 Canada to the US, biological samples were collected from feral swine in
 Alberta (<em>n</em> = 13) and Saskatchewan
 (<em>n</em> = 14), Canada by the University of Saskatchewan
 under Animal Use Protocol Number 21050024. DNA extraction was performed by
 GeneSeek (Neogen Corporation [Lincoln, Nebraska, USA]) using various
 biological sample types (hair, pinna, and kidney) and the
 MagMax<sup>TM </sup>DNA Multi-Sample Ultra Kit (Thermo Fisher
 Scientific Inc. [Walthan, MA, USA]). Genetic samples were genotyped using
 GeneSeek’s Genomic Profiler (GGP) for the Porcine 80k array (68,516 loci;
 Illumina BeadChip microarray [San Diego, California] licensed exclusively
 to GeneSeek, a Neogen Corporation, [Lincoln, Nebraska]) and aligned to the
 Sscrofa 11.1 genome assembly (Warr et al. 2020). As
 part of our quality control process, we removed individuals presumed to
 have escaped or released domestic pigs from production farms or the pet
 trade (i.e., Vietnamese potbellied pigs). To distinguish domestic pigs
 from genetically typical feral swine, we estimated the ancestry profiles
 of individuals based on the methods described in Smyser et al. (2020) and
 removed any individual with a combined ancestry of &gt;0.4 from
 domestic pig breeds (Berkshire, Hampshire, Chester White, Duroc, Landrace,
 Yorkshire/Large White, Meishan, and miniature Siberian). Once individuals
 presumed to be escaped or released domestic pigs were removed, we
 conducted standard genotype quality control filters using PLINK 2.0 (Chang
 et al. 2015). First, we removed loci that were unmapped or non-autosomal
 based on the Sscrofa11.1 reference genome assembly (Warr et al., 2020). We
 then removed loci with call rates &lt;0.95 or minor allele frequencies
 &lt;0.05. Individuals were removed for downstream analyses if they
 were missing &gt;5% of their genotype data. The resulting set of
 individual genotypes was considered the ‘master’ dataset.
description: # Feral swine genotypes and metadata used for identifying translocations
 in the United States
 [https://doi.org/10.5061/dryad.b2rbnzsq9](https://doi.org/10.5061/dryad.b2rbnzsq9) This data contains 35,141 single nucleotide polymorphisms (SNPs) for 18,248 individual feral swine sampled across the contiguous United States as well as 27 feral swine sampled in Canada (Alberta=13 and Saskatchewan=14). We also provide metadata containing the subject ID, the state and county from which the feral swine was sampled, as well as the genetic cluster it was assigned for downstream analyses. ## Description of the data and file structure Genotype data is contained in .bed, .bim, .fam format with the prefix "MasterDatabase GenoData Giglio etal2024 pruned". The metadata is saved as a .csv and named "MasterDatabase MetaData Giglio etal2024.csv". ## Sharing/Access information Wild boar genotypes were derived from the following sources: * Yang, Bin et al. (2018). Data from: Genome-wide SNP data unveils the globalization of domesticated pigs [Dataset]. Dryad. [https://doi.org/10.5061/dryad.30tk6](https://doi.org/10.5061/dryad.30tk6)