DOI: 10.5061/dryad.cz8w9gj49
title: Rooting out genetic structure of invasive wild pigs in Texas

description: Invasive wild pigs (Sus scrofa), also called feral swine or wild hogs, are
 recognized as among the most destructive invasive species in the world.
 Throughout the United States, invasive wild pigs have expanded rapidly
 over the past 30 years with populations now established in 38 states. Of
 the estimated 6.9 million wild pigs distributed throughout the United
 States, Texas supports approximately 40% of the population and similarly
 bears disproportionate ecological and economic costs. Genetic analyses are
 an effective tool for understanding invasion pathways and tracking
 dispersal of invasive species such as wild pigs and have been used
 recently in California and Florida, USA, which have similarly
 long-established populations and high densities of wild pigs. Our goals
 were to use molecular approaches to elucidate invasion and migration
 processes shaping wild pig populations throughout Texas, compare our
 results with patterns of genetic structure observed in California and
 Florida, and provide insights for effective management of this invasive
 species. We used a high-density single nucleotide polymorphism (SNP) array
 to evaluate population genetic structure. Genetic clusters of wild pigs
 throughout Texas demonstrate 2 distinct patterns: weakly resolved,
 spatially dispersed clusters and well-resolved, spatially localized
 clusters. The disparity in patterns of genetic structure suggests
 disparate processes are differentially shaping wild pig populations in
 various localities throughout the state. Our results differed from the
 patterns of genetic structure observed in California and Florida, which
 were characterized by localized genetic clusters. These differences
 suggest distinct biological and perhaps anthropogenic processes are
 shaping genetic structure in Texas. Further, these disparities demonstrate
 the need for location-specific management strategies for controlling wild
 pig populations and mitigating associated ecological and economic costs.
description: We obtained a variety of sample types (i.e., hair, pinna, and
 kidney) collected across 101 Texas counties from euthanized wild pigs that
 were sampled ancillary to population reduction and damage mitigation
 conducted by the United States Department of Agriculture (USDA) Animal and
 Plant Health Inspection Service (APHIS) Wildlife Services (WS) Feral Swine
 Damage Management Program between May 2012 and March 2019. We submitted
 samples to the National Feral Swine Genetic Archive (USDA APHIS WS
 National Wildlife Research Center) for analysis along with corresponding
 metadata, which included sex, age class, date of collection, and
 collection location (county and spatial coordinates rounded to the
 hundredth of a degree to protect the anonymity of private landowners while
 providing spatial accuracy within ~1.1 km). Given that genetic samples
 were collected secondarily to legally authorized control of wild pigs,
 sample collection was exempted from Institutional Animal Care and Use
 Committee review. We extracted genomic DNA with a
 commerically available magnetic bead recovery kit (MagMax, Thermo Fisher
 Scientific, Waltham, MA, USA) using the MagMax Processor (Applied
 Biosystems, Waltham, MA, USA). We then genotyped samples using the
 GeneSeek Genomic Profiler for Porcine HD (GeneSeek, a Neogen Corporation,
 Lincoln, NE, USA; Illumina, San Diego, CA, USA), a commerically available
 genotyping array with 62,128 biallelic, autosomal single nucleotide
 polymorphism (SNP) mapped to the SScofa 11.1 genome assembly (Warr et al.
 2019). We used SNP & Variation Suite version 8.8.3 (Golden Helix,
 Bozeman, MT, USA) to implement standard quality control measures for SNP
 data. Specifically, we pruned loci with low call rates (&lt;95%) and
 minor allele frequencies (MAF) &lt;0.05 (11,800 loci pruned), then
 removed individuals with low genotype call rates (&lt;95%; 25 samples
 pruned) and finally, evaluated linkage disequilibrium (LD) among markers
 and pruned closely linked loci
 (<i>r</i><sup>2</sup> &gt; 50%; window size =
 50, window increment = 5) within chromosomes (20,505 loci
 pruned).